title: Jurkat shTAL1 TAL1-short 1

value: silenced endogenous TAL1 by stable transfection of inducible TAL1 shRNA targeting its 3' UTR


title: HighOVA_1

status: Public on Apr 30 2023

type: SRA

city: Geneva

first: Liqing

last: Cheng

address: 1 rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

library_source: transcriptomic

data_processing:
Read were mapped to the UCSC mm10 mouse genome with STAR v.2.7.4.
The biological QC was performed with picard tools
Table of counts was prepared with HTseq v0.9.1.
After normalization, the differential expression analysis was performed with the package edgeR (v1.34.1) in R.
PCA were obtained using Deseq2
Assembly: UCSC mm10 mouse genome
Supplementary files format and content: txt file containing raw counts of each sample (naïve, mLN, LILP)
Supplementary files format and content: excel file containing raw counts of each sample (highOVA, lowOVA)

molecule: total RNA

organism: Mus musculus

source_name: large intestine lamina propria

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
Nextera Smarter following manufacture's protocol

tag: tissue

value: large intestine lamina propria

tag: cell type

value: transferred CD45.1+CD8+ OTI T cells

tag: genotype

value: WT

tag: Sex

value: Female

tag: treatment

value: Lm-OVA infection in recipient mice


title: Omasum2, Day60

city: Chengdu

first: Li

middle: yi

last: Liu

state: None Selected

address: #16, South Section, 1st Ring Road, Chengdu, Sichuan, China, Post Code 610041

country: China

institute: Southwest Minzu University

data_processing:
Raw data (raw reads) were processed using Trimmomatic.
The raw reads containing ploy-N and the low-quality reads were removed to obtain the clean reads.
FPKM value of each gene was calculated using cufflinks, and the number of reads mapped to each gene was counted by htseq-count.  For transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress.
The reads were reassembled using StringTie. Then the gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile.
Assembly: BosGru_v2.0
Supplementary files format and content: report_Filtered_data_stat-Rum, Ret, Oma, Abo
Supplementary files format and content: counts_anno-Rum, Ret, Oma,Abo
Supplementary files format and content: FPKM_anno-Rum, Ret, Oma, Abo

organism: Bos grunniens

source_name: Omasum

extract_protocol:
The total RNA of each sample was extracted using the mirVana miRNA Isolation Kit (Ambion-1561) following the manufacturer’s instructions.
The libraries were constructed following the manufacturer’s protocol at Shanghai OE Biotech (Shanghai, China), using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) .

value: Omasum

value: Day 60


title: Abomasum2, Day20

source_name: Abomasum

value: Abomasum

value: Day 20


title: Jurkat shTAL1 Empty 3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
The processed reads were aligned with TopHat , allowing for 5 mismatches to the reference human genome  GRCh38, with annotations from Ensembl release 106.
Quantification was done with htseq-count
Normalization, quality control plots (PCA, MA-plots) and differential expression analysis were performed using the DESeq2 package
Pair-wise comparisons were tested with default parameters using the Wald test, without using the independent filtering algorithm. Significance threshold was taken as p-adj<0.1. In addition, significant genes were further filtered by the log2(fold change) value. This filtering was baseMean-dependent and required a baseMean above 5 and an absolute log2FoldChange higher than 5/sqrt(baseMean) + 0.3.for highly expressed genes this means a requirement for a fold-change of at least 1.2, while genes with a very low expression would need a 5.8 -fold change to pass the filtering
Assembly: GRCh38, with annotations from Ensembl release 106
Supplementary files format and content: DESeq2 normalized base mean conts per gene ( ensembl gene id, Symbol) per samples

organism: Homo sapiens

source_name: T-cell

growth_protocol: The experiments described in this manuscript were approved by the Soroka Medical Center, Beer sheva, under IRB-SCRO protocol 0005-14-SOR. iPSCs were cultured on Matrigel-coated 6-well plates in with daily replacements of Nutristem (Biological Industries, Ltd). Cells were cultured at 37°C and 5% CO2. Cells were passaged weekly using EZ-Lift (Millipore) according to the manufacturer’s instructions.

extract_protocol:
Total RNA Purification kit (Norgen Biotek Corp.)
KAPA Stranded mRNA-seq Kit (Roche)

value: T-cell

tag: cell line

value: Jurkat

value: over expression of empty vector


title: Jurkat shTAL1 Empty 2

treatment_protocol: The experiments described in this manuscript were approved by the Soroka Medical Center, Beer sheva, under IRB-SCRO protocol 0005-14-SOR. iPSCs were cultured on Matrigel-coated 6-well plates in with daily replacements of Nutristem (Biological Industries, Ltd). Cells were cultured at 37°C and 5% CO2. Cells were passaged weekly using EZ-Lift (Millipore) according to the manufacturer’s instructions.


title: Omasum1, Day60


title: Abomasum1, Day20


title: Omasum3, Day20


title: Jurkat shTAL1 Empty 1


title: Omasum2, Day20


title: Omasum1, Day20


title: maSARS-CoV-2 infected;  IPI549 treated QD days 2-4 (Biol rep 1) [198]

city: La Jolla

first: Judith

middle: Anne

last: Varner

state: CA

address: Center for Novel Therapeutics 9310 Athena Circle 9310 Athena Circle

department: Pathology

country: USA

institute: University of California, San Diego

description:
PE100 reads
Total Gene Counts.xlsx
Mouse_SarsCov2_RNAseq_rlog_and_DESeq2.xlsx

data_processing:
Quality trimming of fastq files was performed using Trimmomatic (v0.36). Paired-end reads were aligned to the mouse reference genome (GRCm39; annotation file, vM29) using STAR (v2.5.3a), followed by RSEM (v1.3.0) to quantify expression levels of transcripts.
The R BioConductor package DESeq2 was used to perform differential gene expression analysis from unnormalized counts. Lowly expressed genes – defined as those genes with mean <10 reads across all samples – were excluded prior to differential expression analysis.
Significance was defined by using an adjusted p-value cut-off of <0.05 after multiple testing corrections.
Total differentially expressed genes or genes differentially expressed in multiple group comparisons were extracted for gene annotation and functional enrichment analysis using GSEA (Subramanian, Tamayo, et al. 2005; and Mootha, Lindgren, et al. 2003) and Metascape (Zhou et al. 2019).
Assembly: mouse reference genome (GRCm39; annotation file, vM29)
Supplementary files format and content: tab-delimited text files of gene counts for each Sample in  batch and total samples form

source_name: Lung

extract_protocol:
RNA was extracted from mouse SARS-CoV-2 infected lung tissues: The right lung was weighed, bead-homogenized for 5 min in 0.3 ml modified Eagle’s Medium (MEM) and two aliquots of 0.1 mL of homogenate added to 1 ml Trizol prepared and frozen until processing for RNA extraction.  RNA was extracted for cDNA library preparation according Trizol standard methods.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus following manufacturer's protocols.

treatment_protocol: Balb/c female mice 10 months of age were sham infected or infected with ma-SARS-CoV-2 and treated with vehicle or 15 mg/kg IPI-549 for 0-2 or 2-4 days.

tag: strain

value: Balb/c

tag: gender

tag: age

value: 10 months

value: Lung

tag: infection

value: IPI-549  QD days 2-4

tag: molecule subtype

value: total RNA with rRNA depletion


title: HUH6 UBE2C siRNA, 2

city: Helsinki

first: Ruth

last: Nousiainen

address: Tuhkolmankatu 8

country: Finland

institute: University of Helsinki

data_processing:
Chipster (https://chipster.rahtiapp.fi/)
Preprocessing using Trimmomatic
Alignment to human reference genome (GRCh38) using HISAT2
Reads per genes were counted with HTseq
Assembly: GRCh38
Supplementary files format and content: HUH6_results_raw_counts.txt tab-delimited text file includes RPKM values for each sample

source_name: liver

extract_protocol:
The cells were exposed to 25 nM UBE2C ON-TARGETplus SMARTpool siRNA (cat# L-004693-00-0005) or ON-TARGETplus non-targeting (NT) control siRNA (cat# D-001810-10-05; both purchased from Horizon Discovery, Cambridge, UK). Dharmafect 4 (Horizon Discovery) was used to deliver the siRNAs into the HUH6 cells using the protocol provided.
Total RNA and protein was extracted using NucleoSpin RNA/Protein extraction kit (Macherey-Nagel, Düren, Germany). Instructions provided by the manufacturer were followed.
RNA libraries were constructed applying polyA selection, and Illumina compatible cDNA libraries were prepared by GENEWIZ (Leipzig, Germany)

value: liver

value: pediatric hepatoblastoma cells

value: UBE2C siRNA transfection

value: UBE2C knockdown

tag: time


title: Omasum3, Day0

value: Day 0


title: maSARS-CoV-2 infected;  IPI549 treated QD days 2-4 (Biol rep 2) [199]

value: Female

value: WT


title: maSARS-CoV-2 infected; IPI549 treated QD days 0-2 (Biol rep 8) [195]

value: IPI-549 QD days 0-2


title: HUH6 UBE2C siRNA, 3


title: maSARS-CoV-2 infected; IPI549 treated QD days 0-2 (Biol rep 6) [177]


title: Omasum2, Day0

value: Omasum


title: HUH6 UBE2C siRNA, 1


title: maSARS-CoV-2 infected; IPI549 treated QD days 0-2 (Biol rep 7) [176]


title: HUH6 UBE2C siRNA, 4


title: maSARS-CoV-2 infected; IPI549 treated QD days 0-2 (Biol rep 5) [162]


title: HUH6 non-targeting siRNA, 4

value: non-targeting siRNA transfection

value: control


title: maSARS-CoV-2 infected; IPI549 treated QD days 0-2 (Biol rep 4) [194]


title: Reticulum2, Adult

source_name: Reticulum

value: Reticulum

value: Adult


title: Reticulum3, Adult


title: HUH6 non-targeting siRNA, 2


title: HUH6 non-targeting siRNA, 1


title: maSARS-CoV-2 infected; IPI549 treated QD days 0-2 (Biol rep 1) [154]

value: Balb/c

value: 10 months


title: maSARS-CoV-2 infected; IPI549 treated QD days 0-2 (Biol rep 2) [181]

value: Lung


title: maSARS-CoV-2 infected; IPI549 treated QD days 0-2 (Biol rep 3) [175]

value: total RNA with rRNA depletion


title: Reticulum1, Adult


title: HUH6 non-targeting siRNA, 3

value: liver


title: Reticulum3, Day15m

value: Day 15m


title: Reticulum2, Day15m


title: maSARS-CoV-2 infected Vehicle treated QD days 0-2 (Biol rep 5) [179]

value: Vehicle QD days 0-2


title: maSARS-CoV-2 infected; Vehicle treated QD days 0-2 (Biol rep 4) [173]


title: maSARS-CoV-2 infected; Vehicle treated QD days 0-2 (Biol rep 3) [172]


title: Reticulum1, Day15m


title: Reticulum3, Day60

value: Day 60


title: Donor_2_Ctrl_rep2 [Sample_S5-Ctrl-2]

city: New York

first: David

last: Oliver

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
fastp -q 15 -n 10 -l 20 –detect_adapter_for_pe  -i target_R1.fastq -I target_R2.fastq (fastp v0.19.10)
STAR --readFilesIn target_R1.fastq target_R2.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode_v33.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - | samtools markdup -l 800 -rs – target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
featureCounts -p -a gencode_v33.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
Assembly: hg38
Supplementary files format and content: Tab delimited file of gene counts per sample

molecule: polyA RNA

source_name: blood

growth_protocol: Monocytes were cultured overnight at 37oC, 5% CO2 in RPMI-1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone Fisher), penicillin-streptomycin (Invitrogen), L-glutamine (Invitrogen) and 20 ng/ml human M-CSF. after at least 12 hr culture,

extract_protocol:
cell were harvested and total RNA were extreacted using Rneasy Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human monocytes was pretreated with NSA itself or NSA+GSK'872 and then stimulated with CXCL4 (10 µg)and TLR8 ligand ORN8L (20 µg) for 6 h.

value: blood

value: primary monocytes

tag: subject status

value: healthy donor


title: Donor_3_Ctrl_rep3 [Sample_S9-Ctrl-3]


title: Donor_2_cxcl_8L_NSA_GSK872_rep2 [Sample_S8-cxcl4-8L-NSA-GSK872-2]


title: Donor_2_cxcl4_8L_NSA_rep2 [Sample_S7-cxcl4-8L-NSA-2]


title: maSARS-CoV-2 infected; Vehicle treated QD days 0-2 (Biol rep 2) [188]

value: Female

value: WT


title: sitfeb/sitfe3; sgKeap1-2_4

city: Melbourne

first: Andrew

last: Cox

state: Victoria

address: 305 Grattan St

country: Australia

institute: PeterMacCallum Cancer Centre

data_processing:
QC, alignment, and counting were performed in Galaxy.
Sample QC was performed using FastQC (v0.72). Reads were trimmed using Cutadapt (v1.16)
Reads were mapped to human genome (Ensembl hg38) using RNA STAR (v2.7.5b)
Counting was performed using featurecounts (v1.6.3)
Differentially expressed genes were identified using Degust (Limma-Voom v3.40.6)
Assembly: Reads were mapped to human genome (Ensembl hg38).
Supplementary files format and content: Count file generated by featureCounts

growth_protocol: Cells were maintained in EMEM and seeded in 6-well plates.

extract_protocol:
RNA was extracted using the Macherey-Nagel Nucleospin RNA mini kit.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).

treatment_protocol: Cells were transfected with siRNAs and RNA was extracted 72h after transfection.

value: liver cancer

value: sitfeb/sitfe3; sgKeap1-2


title: Reticulum2, Day60

value: Reticulum


title: maSARS-CoV-2 infected; Vehicle treated QD days 0-2 (Biol rep 1) [165]


title: Reticulum1, Day60


title: Donor_2_cxcl4_8L_rep2 [Sample_S6-cxcl4-8L-2]

value: unstimulated


title: Sham infected (biol rep 4) [180]

value: Balb/c

value: Vehicle QD days 0-4


title: Omasum1, Day0

value: Omasum

value: Day 0


title: Donor_1_cxcl_8L_NSA_GSK872_rep1 [Sample_S4-cxcl4-8L-NSA-GSK872-1]


title: sitfeb/sitfe3; sgCtrl_4

value: sitfeb/sitfe3; sgAAVS168


title: Donor_1_cxcl4_8L_NSA_rep1 [Sample_S3-cxcl4-8L-NSA-1]


title: Reticulum3, Day20

value: Day 20


title: Sham infected (biol rep 3) [184]

value: 10 months

value: Lung

value: total RNA with rRNA depletion


title: siNC; sgKeap1-2_4

value: siNC; sgKeap1-2


title: Reticulum2, Day20


title: Donor_1_cxcl4_8L_rep1 [Sample_S2-cxcl4-8L-1]

value: blood

value: primary monocytes

value: healthy donor


title: siNC; sgKeap1-1_4

value: liver cancer

value: siNC; sgKeap1-1


title: Donor_4_cxcl_8L_NSA_GSK872_rep4 [Sample_S16-cxcl4-8L-NSA-GSK872-4]


title: Sham infected (biol rep 2) [169]

value: Female

value: WT


title: Reticulum1, Day20

value: Reticulum


title: Sham infected (biol rep 1) [158]

value: Balb/c

value: Vehicle QD days 0-4


title: siNC; sgCtrl_4

value: siNC; sgAAVS168


title: Donor_4_cxcl4_8L_NSA_rep4 [Sample_S15-cxcl4-8L-NSA-4]


title: sitfeb/sitfe3; sgKeap1-2_3

value: sitfeb/sitfe3; sgKeap1-2


title: Reticulum3, Day0

value: Day 0


title: Reticulum2, Day0


title: Donor_4_cxcl4_8L_rep4 [Sample_S14-cxcl4-8L-4]


title: Donor_4_Ctrl_rep4 [Sample_S13-Ctrl-4]

value: unstimulated


title: Donor_3_cxcl4_8L_NSA [Sample_S11-cxcl4-8L-NSA-3]


title: Rumen3, Adult

source_name: Rumen

value: Rumen

value: Adult


title: sitfeb/sitfe3; sgCtrl_3

value: sitfeb/sitfe3; sgAAVS168


title: siNC; sgKeap1-2_3

value: siNC; sgKeap1-2


title: sitfeb/sitfe3; sgKeap1-1_3

value: sitfeb/sitfe3; sgKeap1-1


title: Donor_3_cxcl_8L_NSA_GSK872_rep3 [Sample_S12-cxcl4-8L-NSA-GSK872-3]

value: blood

value: primary monocytes

value: healthy donor


title: Reticulum1, Day0


title: Rumen2, Adult


title: sitfeb/sitfe3; sgKeap1-1_4

value: liver cancer


title: siNC; sgKeap1-1_3

value: siNC; sgKeap1-1


title: siNC; sgCtrl_3


title: Rumen1, Adult


title: Donor_3_cxcl4_8L [Sample_S10-cxcl4-8L-3]


title: Rumen3, Day15m

value: Day 15m


title: sitfeb/sitfe3; sgKeap1-2_2


title: sitfeb/sitfe3; sgKeap1-1_2


title: Rumen1, Day15m


title: Breast tumor 3, stiff gel, rep2 [B43303]

city: San Francisco

first: Valerie

middle: M

last: Weaver

address: 513 Parnassus Avenue, HSE 560

department: Surgery

institute: UCSF

data_processing:
RNAseq fastq files were mapped to the primary assembly of the Gencode v33 human genome using Rsubread (version 2.0.1) and counted using featureCounts
Lowly expressed genes were filtered out if they did not have at least one CPM in at least 4 samples
Data normalization was performed using calcNormFactors in edgeR (version 3.28.1)
Gene ontology was performed using Gage (version 2.36.0) with gene lists from MsigDB version 7.2
Genome_build: hs33
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Gene ontology table with p-values, q-values, and set sizes for each term enriched in soft or stiff collagen gels

source_name: Human breast tumor cells implanted into mouse

growth_protocol: Rat tail collagen-1 (High concentration, Corning, Cat. #: 354249) was incubated with 0.1% acetic acid or 0.1%acetic acid (non-crosslinked; SOFT) with 2500mM L-ribose (Chem Impex International, Cat. #: 28127) (cross-linked; STIFF) for at least 10 days before preparation of collagen/reconstituted basement membrane (rBM) hydrogels for orthotopic implantation of tumor cells or tumor fragments26,48. Collagen-1 mixtures were then combined with basement membrane extract (R&D Systems, Cultrex BME, type 2, Pathclear, Cat. #: 3532-005-02) (20% final volume), PBS and 1N NaOH to a slightly acidic pH (pH ~6.5) as determined by pH strips. For PDX tissues, collagen/rBM with and without L-ribose was injected orthotopically into a cleared inguinal fat pad and allowed to set for 3-5 minutes prior to implantation of a PDX tissue fragment approximately 2x2mm in size.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen, Cat. #: 15596018) followed by chloroform extraction.
RNAseq library preparation and sequencing was performed by the Vincent J. Coates Genomics Sequencing Laboratory, University of California, Berkeley. Samples were sequenced in NovaSeq 6000 S4 lanes with 150bp paired-end reads with approximately 25 million read pairs per sample.

treatment_protocol: soft and stiff tumors from three different patient-derived xenografts, 3 replicates of each

tag: original patient-derived tumor number

tag: soft or stiff collagen gel

value: stiff

tag: replicate


title: sitfeb/sitfe3; sgCtrl_2


title: Rumen3, Day60

value: Day 60


title: Brain, LHA, 23 dpi, IVA infected

city: København N

first: Birgitte

last: Rahbek Kornum

address: Blegdamsvej 3B

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using the 10x Genomics Cell Ranger version 3.0 pipeline. subsequent read quantification was performed using the Salmon pipeline. Each library underwent separate quality control steps as described in the Alevin pipeline.
Hash-tagged antibody tag oligos (HTO) filtering removes nuclei with low tags or noisy cells. Furthermore, nuclei containing two or more cell barcodes (doublets) were removed.
Cells were tested for their mitochondrial RNA content and outliers with high mitochondrial RNA were removed using the quality control (QC) functions (perCellQCMetrics, PercentageFeatureSet, quickPerCellQC, isOutlier) from the R package scuttle (McCarthy et al., 2017). Counts were normalized using a log transformation of a genes counts divided by the total counts of a cell multiplied by 1e6.
Assembly: mm10
Supplementary files format and content: csv file format
Supplementary files format and content: containf raw and log normalized RNA counts, as well as counts and normalized count after normalization and variance stabilization using regularized negative binomial regression (SCTransform)

source_name: Brain (LHA)

extract_protocol: Libraries were prepared using the 10x Genomics Chromium single-cell 3' reagent kits (version 2). Libraries were sequenced on an Illumina NovaSeq 6000 platform. Nuclei were purified with reagents from the Nuclei Pure Prep Nuclei Isolation Kit (Sigma-Aldrich, NUC-201). See article for details.

value: Brain (LHA)

value: female

value: 13 - 14 weeks

tag: disease

value: H1N1 A/California/07/2009

value: intranasal IVA infection

value: 23 days post infection

tag: number of_animals


title: siNC; sgKeap1-2_2

tag: cell type


title: Brain, LHA, 23 dpi, Control

tag: tissue

value: Control

value: Control (collected at 23 dpi)


title: Rumen2, Day60

value: Rumen


title: Brain, LHA, 7 dpi, IVA infected

tag: Sex

value: 11 - 12 weeks

value: 7 days post infection


title: Brain, LHA, 3 dpi, IVA infected

value: 10 - 11 weeks

tag: treatment

value: 3 days post infection


title: Breast tumor 3, soft gel, rep3 [B43204]

value: soft


title: Breast tumor 3, soft gel, rep1 [B43202]


title: Breast tumor 2, stiff gel, rep3 [H12805]


title: sitfeb/sitfe3; sgKeap1-2_1

tag: cell line

value: liver cancer

value: sitfeb/sitfe3; sgKeap1-2


title: siNC; sgCtrl_2

value: siNC; sgAAVS168


title: Rumen2, Day20

value: Day 20


title: 1792-JL-30

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the mouse reference genome mm10 using STAR
Number of reads for each gene was counted using HTSeq
Assembly: mm10
Supplementary files format and content: raw read count matrix (genes x samples)

source_name: kidney

extract_protocol: To better understand the impact of IL-1β deletion on lupus kidneys, genome-wide transcriptome analysis using RNA-sequencing (RNA-seq) was performed and transcriptional differences in the kidneys of male and female NZM and NZM-Il1b-/- mice were examined

value: kidney

value: Male

tag: genotype

value: WT


title: sitfeb/sitfe3; sgKeap1-1_1

value: sitfeb/sitfe3; sgKeap1-1


title: 1792-JL-29


title: Breast tumor 2, stiff gel, rep2 [H12804]

value: stiff


title: sitfeb/sitfe3; sgCtrl_1

value: sitfeb/sitfe3; sgAAVS168


title: 1792-JL-27

value: Female


title: Donor_1_Ctrl [Sample_S1-Ctrl-1]

value: blood

value: primary monocytes

value: healthy donor

value: unstimulated


title: Breast tumor 3, stiff gel, rep3 [B43304]


title: Rumen2, Day15m

value: Rumen

value: Day 15m


title: Breast tumor 2, stiff gel, rep1 [H12802]


title: Rumen3, Day0

value: Day 0


title: 1792-JL-25


title: Rumen2, Day0


title: siNC; sgKeap1-2_1

value: liver cancer

value: siNC; sgKeap1-2


title: Breast tumor 2, soft gel, rep3 [H12703]

value: soft


title: Breast tumor 3, stiff gel, rep1 [B43104]


title: siNC; sgKeap1-1_1

value: siNC; sgKeap1-1


title: Breast tumor 2, soft gel, rep2 [H12702]


title: 1792-JL-23

value: kidney


title: siNC; sgCtrl_1

value: siNC; sgAAVS168


title: Breast tumor 2, soft gel, rep1 [H12701]


title: siNC; sgKeap1-1_2


title: Breast tumor 3, soft gel, rep2 [B43203]


title: Rumen1, Day60

value: Day 60


title: 1792-JL-22


title: sgKeap1-2-3

extract_protocol:
RNA was extracted 48h after seeding. RNA was extracted using the Macherey-Nagel Nucleospin RNA mini kit.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).


title: Rumen3, Day20

value: Day 20


title: 1792-JL-21

value: WT


title: sgKeap1-1-3


title: H3K27ac_async_2i_4HT_rep2

first: Robert

last: Blelloch

address: 35 Medical Center Way

department: Urology

library_source: genomic

data_processing:
Library strategy: CUT&Tag
Nextflow/ATAC
featureCounts read count in OCT4-SOX2-NANOG overlapped peaks
featureCounts read count at genes nearby OCT4-SOX2-NANOG overlapped peaks
DESeq2 differential enrichment analysis
Genome_build: mm10
Supplementary_files_format_and_content: count matrix

molecule: genomic DNA

source_name: mESCs

growth_protocol: Mouse ESCs were seeded on a well of a 6well plate (170k cells) in L2i containing growth medium.

extract_protocol: Libraries were constructed using custom adaptors according to

treatment_protocol: Phase sorting was performed by DNA content labeling with DAPI.

tag: antibody

value: H3K27ac (Abcam ab4729)

value: mESCs

tag: culture conditions

tag: treatment time


title: Breast tumor 1, stiff gel, rep2 [B63802]

value: stiff


title: 1792-JL-20

value: Female


title: sgCtrl-3


title: H3K27ac_async_2i_4HT_rep1


title: Breast tumor 1, stiff gel, rep1 [B63801]


title: Rumen1, Day20


title: 1792-JL-19


title: sgKeap1-1-2


title: Breast tumor 1, soft gel, rep2 [B63704]


title: 1792-JL-17

value: Male


title: H3K27ac_async_2i_EtOH_rep1


title: sgCtrl-2


title: Breast tumor 1, soft gel, rep1 [B63703]


title: 1792-JL-24


title: FOXD3-endo-ctr-2i-rep2

data_processing:
Bowtie 2 mapping
Deeptools bamCompare for bigwig file creation
Peak calling with MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: Mouse ESCs were seeded on a 10 cm plate (10^6 cells) in L2i containing growth medium and harvested 2 days after seeding.

extract_protocol:
Lysates were clarified from sonicated nuclei and FOXD3-DNA complexes were isolated with streptavidin magnetic beads.
Libraries were prepared according to manufacturers' instructions (NEBNext Ultra II).

treatment_protocol: For exogenous samples, cells were kept consistently on 0.05µg/ml doxycycline for expression of exogenous FOXD3-Avi.

tag: tag insertion

value: endogenous

tag: bait

value: streptavidin magnetic beads


title: 1792-JL-15


title: sgKeap1-2-1


title: FOXD3-endo-ctr-2i-rep1


title: Rumen1, Day0

value: Rumen

value: Day 0


title: 1792-JL-1


title: sgKeap1-1-1

value: liver cancer


title: С_105: blood_Control_exp_5

type: genomic

city: Moscow

first: Liubov

last: Skorodumova

address: Malaya Pirogovskaya st., 1A

country: Russia

institute: Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency

description: Genomic DNA extracted from whole blood was genotyped using Infinium Omni2.5-8 v1.5 Kit (Illumina). Diagnosis, group assignment and CTG18.1 genotyping were conducted according to methods described in Skorodumova et al. (2018; doi: 10.1167/iovs.18-24590).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a iScan array scanner (Illumina).

data_processing:
Genomic DNA was genotyped using Infinium Omni2.5-8 v1.5 Genotyping BeadChips (Illumina).
Image data was analyzed using GenomeStudio 2.0.4 with Genotyping module 2.0.4 (Illumina).

label: Cy3, Cy5

source_name: whole blood DNA

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using Multi-Sample Amplification 1 Mix (WG-MA1), Random Primer Mix (WG-RPM) and Multi-Sample Amplification Master Mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was isolated from thawed blood samples with the Wizard® Genomic DNA Purification Kit (Promega Corp.; Wisconsin, USA) or Gentra Puregene Blood Kit (Qiagen; Germany) according to the manufacturer's protocol.

tag: gender

value: male

tag: age

tag: condition

value: Control group

tag: ctg18.1 repeats expansion status

value: expanded

tag: number of ctg repeats on the smaller allele

tag: number of ctg repeats on the greater allele


title: С_103: blood_Control_exp_4

value: female


title: Breast tumor 1, stiff gel, rep3 [B63803]

tag: original patient-derived tumor number

tag: soft or stiff collagen gel

tag: replicate


title: FOXD3-endo-2i-rep2

tag: cell type


title: S_TAM_Rep1

data_processing:
Nextflow/ATAC
multibigwigsummary at TSS
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

tag: treatment

value: 24h 4HT

tag: cell cycle

value: S


title: FOXD3-endo-2i-rep1


title: sgCtrl-1

tag: cell line


title: ATAC_4HT_G2_rep2

data_processing:
Nextflow/ATAC
featureCounts read count in OCT4-SOX2-NANOG overlapped peaks
DESeq2 differential enrichment analysis
Genome_build: mm10
Supplementary_files_format_and_content: count matrix

tag: culture conditions

tag: genotype


title: С_66: blood_Control_exp_2


title: S_EtOH_Rep2

value: 24h EtOH

tag: treatment time


title: Mesenchymal stem cell, TWIST1-overexpression

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

country: Japan

institute: Kindai Universty Hospital

data_processing:
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina). Obtained reads (CAGE tags) were mapped to the human hg19 genome using BWA (version 0.5.9). Unmapped reads were then mapped by HISAT2 (version 2.0.5).
CAGE tag count data were clustered using the CAGEr (Haberle et al., Nucleic Acids Research 2015, 30:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default parameters. Clusters with count per million (CPM) < 0.2 were discarded.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
The list of differentially expressed genes detected by CAGEr (CPM > 1 and fold-change < 0.25, or CPM > 1 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: hg19
Supplementary files format and content: Empty.control.GFP-Transfected.Tw1_DESeq.txt

source_name: Mesenchymal stem cell

growth_protocol: Cells were cultured in α-MEM supplemented with 200 mM L-glutamine, 10% fetal bovine serum under 5%CO2 and 5%O2 at 37℃.

extract_protocol:
The Nascent RNA was extracted from cells according to the Hirabayashi et al. (2019).
The cDNAs were synthesized from nascent RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

treatment_protocol: GFP or Twist1-overexpression cells were infected with the SeVdp vectors at a MOI of 5 and incubated overnight at 37°C. The viral medium was replaced, and 10 μg/mL puromycin was added to purify the MSCs stably expressing the SeVdp-TWIST1 or GFP

value: Mesenchymal stem cell


title: sgKeap1-2-2


title: С_52: blood_Control_exp_1


title: Mesenchymal stem cell, GFP-overexpression

value: control (GFP)


title: Breast tumor 1, soft gel, rep3 [B63705]

value: soft


title: H3K27ac_async_2i_EtOH_rep2

tag: antibody

value: H3K27ac (Abcam ab4729)

value: mESCs


title: Dfu_11: blood_FECD_noexp_26

tag: gender

value: Fuchs endothelial corneal dystrophy

value: non expanded


title: ATAC_4HT_LS_rep2


title: G2_TAM_Rep2


title: 1792-JL-16

tag: tissue

value: kidney

tag: Sex

value: Male


title: ATAC_4HT_LS_rep1


title: H3FLTBGXC_Gen22_MSC_LG_T2_D86_rep_2

city: Brisbane

first: Atefeh

last: Taherian Fard

address: St Lucia

institute: The University of Queensland

data_processing:
The raw sequence reads, obtained as fastq files were subjected to quality control.
The processed reads were aligned to the human GRCh38 reference genome prebuilt with gene annotations within 10X’s cellranger 3.0.2. software. The alignment was performed using the STAR aligner employed within cellranger 3.0.2
Cellranger (v3.0.2) was used to generate and integrate the unfiltered unique molecular identifier (UMI) count matrix from the nine libraries (three replicates for each of the three time-points). From sequencing an average of 22,609 high quality reads were obtained per cell. Reads were mapped to human GRCh38 genome, and an average of 92% reads was mapped confidently to the transcriptome.
The quantified counts for the raw, unfiltered cell barcodes were stored as a gene x cell matrix and exported for further downstream analyses.
Assembly: human GRCh38 genome
Supplementary files format and content: Processed files is a compressed tar file containing one folder per sample- raw feature barcode matrix from cellranger processing pipeline. Each folder contains barcodes, features and count matrix files.

source_name: hESC derived Mesenchymal Stem Cells

extract_protocol: Single cell suspension was partitioned and barcoded using the 10X Genomics Chromium Controller (10X Genomics) and the Single Cell 3' Library and Gel Bead Kit (V2; 10X Genomics; PN-120237).  The cells were loaded onto the Chromium Single Cell Chip A (10X   Genomics; PN-120236) to target 10,000 cells. GEM generation and barcoding, cDNA amplification, and library construction was performed according to the 10X Genomics Chromium User Guide. The libraries were sequenced on Illumina NextSeq-500.

tag: sequencing run

tag: time point

value: Rep 2

value: hESC line Genea022


title: H3FLTBGXC_Gen22_MSC_LG_T2_D86_rep_3

value: Rep 3


title: G2_TAM_Rep1


title: Dfu_228: blood_FECD_noexp_24

tag: age

tag: condition

tag: ctg18.1 repeats expansion status

tag: number of ctg repeats on the smaller allele

tag: number of ctg repeats on the greater allele


title: H3FLTBGXC_Gen22_MSC_LG_T1_D49_rep_3

tag: replicate


title: G2_EtOH_Rep2

tag: cell type

tag: treatment

tag: cell cycle


title: H3FLTBGXC_Gen22_MSC_LG_T1_D49_rep_2

tag: cell line


title: Dfu_222: blood_FECD_noexp_23


title: G2_EtOH_Rep1

tag: culture conditions

tag: genotype

tag: treatment time


title: ATAC_4HT_ES_rep1


title: S_TAM_Rep2


title: H3FLTBGXC_Gen22_MSC_LG_T0_D23_rep_3


title: Dfu_219: blood_FECD_noexp_22

tag: gender


title: ATAC_4HT_G1_rep2


title: С_68: blood_Control_exp_3

value: Control group

value: expanded


title: H3FLTBGXC_Gen22_MSC_LG_T0_D23_rep_2


title: G1_TAM_Rep2

value: 24h 4HT


title: ATAC_4HT_G1_rep1


title: G1_TAM_Rep1


title: H3FLTBGXC_Gen22_LG_D86

value: Rep 1


title: Dfu_209: blood_FECD_noexp_20

value: female


title: ATAC_EtOH_G2_rep2


title: G1_EtOH_Rep2

value: 24h EtOH


title: H3FLTBGXC_Gen22_LG_D49


title: ATAC_4HT_G2_rep1


title: ATAC_EtOH_G2_rep1


title: G1_EtOH_Rep1


title: H3FLTBGXC_Gen22_LG_D22


title: Dfu_37: blood_FECD_noexp_18

value: male


title: Dfu_103: blood_FECD_noexp_19


title: S_EtOH_Rep1

value: S


title: Dfu_229: blood_FECD_noexp_25


title: ATAC_EtOH_LS_rep2


title: H3FLHBGXC_Gen22_MSC_LG_T2_D86_rep_3


title: Dfu_29: blood_FECD_noexp_17


title: ATAC_4HT_ES_rep2


title: ATAC_EtOH_LS_rep1


title: H3FLHBGXC_Gen22_MSC_LG_T2_D86_rep_2


title: DFu_12: blood_FECD_noexp_16


title: ATAC_EtOH_ES_rep2


title: H3FLHBGXC_Gen22_MSC_LG_T1_D49_rep_3


title: TT_H2BK120ac_rep3

data_processing:
Nextflow/ATAC
multibigwigsummary at atac sites
multibigwigsummary at TSS
Assembly: mm10
Supplementary files format and content: count matrix
Library strategy: CUT&Tag

tag: antibody


title: 210_1: blood_FECD_noexp_14


title: ATAC_EtOH_ES_rep1


title: TT_H2BK120ac_rep2


title: H3FLHBGXC_Gen22_MSC_LG_T1_D49_rep_2

tag: sequencing run


title: ATAC_EtOH_G1_rep2


title: TT_H2BK120ac_rep1


title: 97_2: blood_FECD_noexp_13


title: Dfu_217: blood_FECD_noexp_21


title: H3FLHBGXC_Gen22_MSC_LG_T0_D23_rep_3

tag: time point


title: ATAC_EtOH_G1_rep1


title: 96_1: blood_FECD_noexp_12

tag: age


title: TD_H2BK120ac_rep3


title: 4HT-Thy-5h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG143

data_processing:
Library strategy: 4SU-seq
STAR mapping
featureCounts read count
Genome_build: mm10
Supplementary_files_format_and_content: count matrices

growth_protocol: Mouse ESCs were seeded on a 10 cm plate (10^6 cells) or for synchronized cells on a well of a 6well plate (170k cells) in L2i containing growth medium.

extract_protocol:
Cells were extracted using Trizol LS.
Libraries were prepared according to manufacturers' instructions (KAPA RNA Hyperprep).

treatment_protocol: Synchronization was achieved using a double thymidine block strategy and cells were release at 24h post tamoxifen treatment. 4SU was added for 30min or 15min for non-synchronized and synchronized cells, respectively.

tag: molecule subtype

value: 4SU-labeled RNA


title: 87_2: blood_FECD_noexp_11

tag: condition

tag: ctg18.1 repeats expansion status


title: H3FLHBGXC_Gen22_MSC_LG_T0_D23_rep_2


title: H3FLHBGXC_Gen22_LG_D86


title: 4HT-Thy-4h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG142


title: TD_H2BK120ac_rep1

value: mESCs


title: H3FLHBGXC_Gen22_LG_D49


title: 80_2: blood_FECD_noexp_10

value: Fuchs endothelial corneal dystrophy

tag: number of ctg repeats on the smaller allele

tag: number of ctg repeats on the greater allele


title: 76_1: blood_FECD_noexp_9

value: non expanded


title: H3FLHBGXC_Gen22_LG_D22

tag: replicate


title: ET_H2BK120ac_rep3

tag: cell type


title: 4HT-Thy-2h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG140


title: ET_H2BK120ac_rep2


title: H3FKGBGXC_Gen22_MSC_LG_T2_D86_rep_3


title: 69_1: blood_FECD_noexp_8


title: 4HT-Thy-1h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG139


title: ET_H2BK120ac_rep1


title: H3FKGBGXC_Gen22_MSC_LG_T2_D86_rep_2


title: 62_1: blood_FECD_noexp_7


title: 223_2: blood_FECD_noexp_15


title: 4HT-Thy-0h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG138


title: ED_H2BK120ac_rep3


title: 58: blood_FECD_noexp_6


title: 4HT-Thy-5h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG137


title: H3FKGBGXC_Gen22_MSC_LG_T1_D49_rep_3


title: 57: blood_FECD_noexp_5


title: ED_H2BK120ac_rep2


title: H3FKGBGXC_Gen22_MSC_LG_T1_D49_rep_2


title: 4HT-Thy-4h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG136


title: ED_H2BK120ac_rep1


title: 4HT-Thy-3h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG135


title: 56_1: blood_FECD_noexp_4


title: H3FKGBGXC_Gen22_MSC_LG_T0_D23_rep_3


title: sgBcor + sgLuc rpl3

city: Hannover

first: Dorit

last: Borchert

address: Carl-Neuberg-Str. 1

department: Pediatric Hematology and Oncology

country: Germany

institute: Hannover Medical School

description:
B_L_3
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx

data_processing:
Base calling was performed using standard Illumina software.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. Clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Sequencing reads were aligned to the mouse genome using the HISAT2 tool.
Gene expression was measured by transcript abundance, normalized by the FPKM method, utilizing HTSeq software.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNA_Seq_genes.readcount.annot.xlsx: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: RNA_Seq_genes.FPKM.annot.xlsx: Matrix table with FPKM values for every gene and every sample.

source_name: Murine whole bone marrow

growth_protocol: 1-4x10^4 LSK cells from Cas9 knockin mice were transduced with the given sgRNA combinations and transplanted after 24 h into irradiated (7 Gy) C57Bl/6J mice. Complete BM was harvested after presenting with signs of leukemia or after 6 months.

extract_protocol:
Zymo RNA Micro Kit (Zymo Research No. R1050).
mRNA from eukaryotic organisms is enriched using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

tag: tissue

value: Whole bone marrow

tag: strain

tag: treatment

value: sgBcor + sgLuc


title: H3FKGBGXC_Gen22_MSC_LG_T0_D23_rep_2

value: Rep 2

tag: cell line


title: TD_H2BK120ac_rep2

tag: culture conditions

tag: genotype

tag: treatment time


title: 4HT-Thy-2h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG134


title: H3FKGBGXC_Gen22_LG_D86

tag: sequencing run

value: hESC line Genea022


title: sgBcor + sgLuc rpl2

description:
B_L_2
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: 49_2: blood_FECD_noexp_2

tag: gender


title: sgBcor + sgLuc rpl1

description:
B_L_1
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: 4HT-Thy-1h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG133


title: 50_1: blood_FECD_noexp_3

tag: age


title: 4HT-Thy-3h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG141

tag: molecule subtype


title: H3FKGBGXC_Gen22_LG_D49

tag: time point


title: 45_1: blood_FECD_noexp_1

tag: condition

tag: ctg18.1 repeats expansion status


title: 4HT-Thy-0h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG132


title: sgBcor + sgRunx1 rpl3

description:
B_R_5
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx

value: sgBcor + sgRunx1


title: H3FKGBGXC_Gen22_LG_D22


title: EtOH-Thy-5h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG131


title: H3F5JBGXC_Gen22_MSC_LG_T2_D86_rep_3

value: Rep 3


title: sgBcor + sgRunx1 rpl2

description:
B_R_3
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: EtOH-Thy-4h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG130


title: sgBcor + sgRunx1 rpl1

description:
B_R_2
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H3F5JBGXC_Gen22_MSC_LG_T2_D86_rep_2


title: EtOH-Thy-3h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG129


title: sgEzh2 + sgRunx1 rpl4

description:
E_R_5
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx

value: sgEzh2 + sgRunx1


title: H3F5JBGXC_Gen22_MSC_LG_T1_D49_rep_3


title: EtOH-Thy-2h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG128


title: sgEzh2 + sgRunx1 rpl3

description:
E_R_3
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H3F5JBGXC_Gen22_MSC_LG_T1_D49_rep_2


title: EtOH-Thy-1h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG127


title: sgEzh2 + sgRunx1 rpl2

description:
E_R_2
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H3F5JBGXC_Gen22_MSC_LG_T0_D23_rep_3


title: EtOH-Thy-0h-rep2

description:
counts_foxd3_thymidine_sychronized.txt
DG126


title: EtOH-Thy-5h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG125


title: sgEzh2 + sgRunx1 rpl1

description:
E_R_1
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H3F5JBGXC_Gen22_LG_D86


title: sgEzh2 + sgLuc rpl3

description:
E_L_3
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx

value: sgEzh2 + sgLuc


title: EtOH-Thy-4h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG124


title: sgEzh2 + sgLuc rpl2

description:
E_L_2
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H3F5JBGXC_Gen22_LG_D49

value: Rep 1


title: EtOH-Thy-3h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG123


title: H3F5JBGXC_Gen22_LG_D22


title: EtOH-Thy-2h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG122


title: sgRunx1 + sgLuc rpl3

description:
R_L_3
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx

value: sgRunx1 + sgLuc


title: H2HJKBGXC_Gen22_MSC_LG_T2_D86_rep_3


title: EtOH-Thy-1h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG121


title: H2HJKBGXC_Gen22_MSC_LG_T2_D86_rep_2


title: sgRunx1 + sgLuc rpl2

description:
R_L_2
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: sgRunx1 + sgLuc rpl1

description:
R_L_1
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H2HJKBGXC_Gen22_MSC_LG_T1_D49_rep_3


title: EtOH-Thy-0h-rep1

description:
counts_foxd3_thymidine_sychronized.txt
DG120


title: H2HJKBGXC_Gen22_MSC_LG_T1_D49_rep_2


title: sgLuc rpl6

description:
Luc_6
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx

value: sgLuc


title: sgLuc rpl5

description:
Luc_5
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H2HJKBGXC_Gen22_MSC_LG_T0_D23_rep_3


title: sgLuc rpl4

description:
Luc_4
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H2HJKBGXC_Gen22_MSC_LG_T0_D23_rep_2


title: sgLuc rpl3

description:
Luc_3
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: H2HJKBGXC_Gen22_LG_D86


title: HeLa-CRISPR-Lys

city: Shinjuku-ku

first: Aya

last: Mizuike

state: Tokyo

address: 1-23-1 Toyama

department: Quality Assurance, Radiation Safety and Information System

institute: National Institute of Infectious Diseases

data_processing:
demultiplexing the fastq sequence data, and alignment to sgRNA of Human GeCKO v2 library A/B using CRISPR_process.pl
Genome_build: Human GeCKO v2 library A/B
Supplementary_files_format_and_content: tab-delimited text files include raw read count of each sgRNA

source_name: uterine cervix

growth_protocol: HeLa CAS9#W7 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) with 7.5μg/ml blasticidin . HeLa CAS9#W7 cells were infected with the pooled lentiviruses to express sgRNAs.

extract_protocol:
Genomic DNA from the frozen cells was purified by the conventional phenol-chloroform method.
First PCR amplification was carried out with 20 cycles using PrimeStar GXL DNA polymerase (Takara, Otsu, Japan) and the following primers (9 forward primers and 1 reverse primer): (Fw) 1stY1R1s0-8: CTACACGACGCTCTTCCGATCT[-/N/NN/NNN/NNNN/NNNNN/NNNNNN/NNNNNNN/NNNNNNNN]TCTTGTGGAAAGGACGAAACACCG (included 0-8 bp random sequence for increasing library complexity); and (Rv) 1stY2as: GCCACTTTTTCAAGTTGATAACGGACTAG. Second PCR amplification was carried out with 10 cycles using the following primers: (Fw) 2nd P5R1s: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; and (Rv) 2nd P7Y2as: CAAGCAGAAGACGGCATACGAGAT[CC/TT/AA/GG]GCCACTTTTTCAAGTTGATAACGGACTAG (included barcodes for multiplexing of different samples).
Amplicon sequencing of sgRNA in GeCKO v2.0 library plasmid

treatment_protocol: The sgRNA-expressing cells were treated with 100 ng/ml lysenin for three times in 10 days. Lysenin treatment was performed under FBS-free condition.

value: HeLa

value: treated with lysenin for 2 hr x 3 times


title: HeLa-CRISPR-ctrl

value: untreated


title: H2HJKBGXC_Gen22_LG_D49


title: sgLuc rpl2

description:
Luc_2
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx


title: coumestrol, 24 hours, biological rep2

type: RNA

city: Chapel Hill

first: Kathleen

last: Caron

state: NC

address: 111 Mason Farm Road, CB7545

department: Cell Biology and Physiology

institute: University of North Carolin

hyb_protocol: GeneChips were washed and stained in the  2 GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader

data_processing: Data was analyzed using Partek Genomics Suite with Gene Expression Workflow. The microarray data was analyzed using the RMA Import Settings on Partek Genomics Suite 7.0. The default RMA settings include "Interrogating Probes" to import, with no probe filtering, with RMA Background Correction, Quantile Normalization, a Log Probes using Base number 2, with a Median Polish Probeset Summarization.

label: gene expression data from coumestrol treated (65µM), 24 hour time point, HTR8/Svneo Trophoblast cells

source_name: HTR8/Svneo trophoblast cells

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocol.

growth_protocol: HTR8/Svneo cells were grown and maintained with RPMI-1640 with 5% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol: Cells were washed with sterile PBS. RNA was extracted using the Ambion mirVana miRNA isolation kit with phenol for isolation of total RNA according to manufacturer's instructions (Thermo fisher Scientific #AM1560)

treatment_protocol: For coumestrol treatment, HTR8/Svneo cells were plated onto a 6 well plate using RPMI-1640 without phenol red with 5% fetal bovine serum and 1% penicillin/streptomycin. Upon reaching confluency, cells were treated with media (RPMI-1640 without phenol red with 5% fetal bovine serum and 1% penicillin/streptomycin) containing vehicle or coumestrol (65µM) for 24 hours.

value: trophoblast cells

value: wildtype

tag: agent

value: coumestrol


title: sgLuc rpl1

description:
Luc_1
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx

value: Whole bone marrow


title: H3F5JBGXC_Gen22_MSC_LG_T0_D23_rep_2

tag: replicate


title: H2HJKBGXC_Gen22_LG_D22


title: coumestrol, 24 hours, biological rep3


title: vehicle, 24 hours, biological rep3

label: gene expression data from vehicle treated, 24 hour time point, HTR8/Svneo Trophoblast cells

value: vehicle


title: coumestrol, 24 hours, biological rep1


title: vehicle, 24 hours, biological rep2


title: 786-OGT3

status: Public on Apr 29 2023

city: Shanghai

first: Zhou

last: Yang

state: Shanghai

address: 270 Donan Road

institute: Fudan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

growth_protocol: 786-Ocells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

tag: cell type

value: ccRCC

value: OGT overexpressed


title: 786-OGT2


title: vehicle, 24 hours, biological rep1

tag: tissue


title: 786-NC3

value: WT


title: 786-NC2


title: 786-NC1


title: sgEzh2 + sgLuc rpl1

description:
E_L_1
RNA-Seq data for determination of global gene expression in BM transplanted mice transduced with sgRNA combinations
RNA_Seq_genes.readcount.annot.xlsx
RNA_Seq_genes.FPKM.annot.xlsx

tag: strain


title: 786-OGT1


title: arrayCGH data from patient 3821

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

hyb_protocol: The hybridization mixtures were denatured at 95°C for 3 minutes, preincubated at 37°C for 30 minutes, and hybridized to the array in a microarray hybridization chamber (Agilent Technologies) for 14 to 18 hours at 65°C in a rotating oven (Robbins Scientific, Mountain View, CA). The array slides were washed in 0.5x SSC/0.005% Triton X-102 at room temperature for 5 minutes, followed by 5 minutes at 37°C in 0.1x SSC/0.005% Triton X-102.

scan_protocol: TIF images were obtained using Agilent scanner (model B and C)

data_processing: Images were analyzed using Cytogenomics v.50.0.38 software with the default analysis method: CGH v2 (ADM-2 algortihm). Threshold of 6.0, with a minimum of 3 consecutive aberrant probes and a minimum absolute amplification/deletion average of 0.25 log2ratio

source_name: pediatric patient samples

label_protocol: Labeling reactions with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Wellesley, MA) were performed with 5 μg purified restricted DNA using the Bioprime labeling kit (Invitrogen, Paisley, United Kingdom) according to the manufacturer's instructions. Experimental and reference targets for each hybridization were pooled and mixed with 50 μg human Cot-1 DNA (Invitrogen), 100 μg yeast tRNA (Invitrogen), and 1x hybridization control targets (SP310; Operon Technologies, Alameda, CA) in a final volume of 500 μL in situ hybridization buffer (Agilent Technologies).

extract_protocol: 10 μg genomic reference or patient DNA was digested with AluI (20 U) and RsaI (20 U) (Invitrogen) overnight at 37°C. Patient genomic DNA (2 μg) and male/female reference DNA (2 μg; Promega) were fragmented by sonification (VibraCell Model VC130; Sonics & Materials, Newtown, CT). DNA fragmentation was verified by agarose gel electrophoresis. Individual reference and experimental samples were then purified using the QIAQuick polymerase chain reaction (PCR) clean-up kit (Qiagen, Valencia, CA).

tag: subarray

tag: subject

value: patient 3821

value: control


title: arrayCGH data from patient 3622

value: patient 3622


title: arrayCGH data from patient 3770

value: patient 3770


title: arrayCGH data from patient 3976

value: patient 3976


title: arrayCGH data from patient 4023

value: patient 4023


title: arrayCGH data from patient 2460

value: patient 2460


title: arrayCGH data from patient vu9827

value: patient vu9827


title: arrayCGH data from patient 5669

value: patient 5669


title: arrayCGH data from patient 5438

value: patient 5438


title: arrayCGH data from patient 9247

value: patient 9247


title: arrayCGH data from patient 5676

value: patient 5676


title: arrayCGH data from patient 4981

value: patient 4981


title: arrayCGH data from patient vu9989

value: patient vu9989


title: arrayCGH data from patient 5673

value: patient 5673


title: arrayCGH data from patient vu9696

value: patient vu9696


title: arrayCGH data from patient 3594

value: patient 3594


title: arrayCGH data from patient vu9105

value: patient vu9105


title: arrayCGH data from patient 4068

value: patient 4068

value: control


title: arrayCGH data from patient 5716

value: patient 5716


title: arrayCGH data from patient vu10138

value: patient vu10138


title: arrayCGH data from patient 3645

value: patient 3645


title: arrayCGH data from patient vu9919

value: patient vu9919


title: genomic DNA from patient 1946

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: Data was processed using the packages: minfi_1.38.0  and meffil_1.1.2

label: Cy3 and Cy5

source_name: Patient Derived Xenograft

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: ctcf status

value: CTCF Mutated


title: arrayCGH data from patient vu9963

value: patient vu9963


title: genomic DNA from patient 5676

value: CTCF Deletion


title: genomic DNA from patient 9757

value: CTCF Wild Type


title: genomic DNA from patient 2436


title: genomic DNA from patient 1179


title: arrayCGH data from patient 2805

value: patient 2805


title: genomic DNA from patient 719


title: arrayCGH data from patient 2794

value: patient 2794


title: arrayCGH data from patient vu9376

value: patient vu9376


title: arrayCGH data from patient vu9027

value: patient vu9027


title: genomic DNA from patient 3977


title: genomic DNA from patient 634


title: arrayCGH data from patient 1632B

value: patient 1632B


title: arrayCGH data from patient vu9194

value: patient vu9194


title: arrayCGH data from patient 1113

value: patient 1113


title: arrayCGH data from patient 1509

value: patient 1509


title: arrayCGH data from patient vu9160

value: patient vu9160

value: control


title: arrayCGH data from patient 2436

value: patient 2436


title: arrayCGH data from patient 1570

value: patient 1570


title: arrayCGH data from patient 2252

value: patient 2252


title: arrayCGH data from patient 2130

value: patient 2130


title: arrayCGH data from patient vu9577

value: patient vu9577


title: arrayCGH data from patient vu10030

value: patient vu10030


title: arrayCGH data from patient 1815

value: patient 1815


title: arrayCGH data from patient 3044

value: patient 3044


title: arrayCGH data from patient vu8577

value: patient vu8577


title: arrayCGH data from patient vu9226

value: patient vu9226


title: arrayCGH data from patient vu8639

value: patient vu8639


title: arrayCGH data from patient 2911

value: patient 2911


title: arrayCGH data from patient 2322

value: patient 2322


title: arrayCGH data from patient 492

value: patient 492


title: arrayCGH data from patient 1964

value: patient 1964


title: arrayCGH data from patient 167

value: patient 167


title: arrayCGH data from patient 321

value: patient 321

value: control


title: arrayCGH data from patient 1132

value: patient 1132


title: arrayCGH data from patient 1524

value: patient 1524


title: arrayCGH data from patient 491

value: patient 491


title: arrayCGH data from patient 344

value: patient 344


title: arrayCGH data from patient 2229

value: patient 2229


title: arrayCGH data from patient vu9012

value: patient vu9012


title: arrayCGH data from patient vu9928

value: patient vu9928


title: arrayCGH data from patient vu10110

value: patient vu10110


title: arrayCGH data from patient vu9938

value: patient vu9938


title: arrayCGH data from patient vu10111

value: patient vu10111


title: arrayCGH data from patient 2120

value: patient 2120


title: arrayCGH data from patient 2669

value: patient 2669


title: arrayCGH data from patient vu8628

value: patient vu8628


title: arrayCGH data from patient 1753

value: patient 1753


title: arrayCGH data from patient vu8815

value: patient vu8815


title: arrayCGH data from patient 750

value: patient 750


title: arrayCGH data from patient 2702

value: patient 2702

value: control


title: arrayCGH data from patient 1948

value: patient 1948


title: arrayCGH data from patient vu9083

value: patient vu9083


title: arrayCGH data from patient 759

value: patient 759


title: arrayCGH data from patient 2775

value: patient 2775


title: arrayCGH data from patient vu9323

value: patient vu9323


title: P8_S256

city: Huddinge

first: Ping

last: Chen

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Mouse non-parenchymal single cells

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads were aligned to human genome mm10 using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 20% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; 4) >= 1000 genes with RPKM >= 1; and 5) < 25% of mitochondrial gene expression. In addition, doublets detected by Scrublet were further removed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each single cell.

source_name: Mouse non-parenchymal single cells

growth_protocol: Not applicable

extract_protocol:
Not applicable
The reverse-transcribed cDNA from single cells was amplified followed by tagmentation and a standard index PCR. The single cell libraries were prepared according to Smart-seq2 protocol. The sequencing was performed on HISEQ 3000 (IIlumina).
Smart-seq2 single cell RNA-Seq

treatment_protocol: Not applicable

value: Liver

tag: disease state


title: P5_S232

description: Mouse non-parenchymal single cells


title: P9_S264

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 2486

value: patient 2486


title: arrayCGH data from patient 2641

value: patient 2641


title: P3_S216

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 2792

value: patient 2792


title: P1_S200

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 2703

value: patient 2703


title: arrayCGH data from patient 2846

value: patient 2846


title: P6_S240

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 2748

value: patient 2748


title: P20_S352

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 572

value: patient 572


title: P19_S344

description: Mouse non-parenchymal single cells


title: P16_S320

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 914

value: patient 914


title: P14_S304

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 540

value: patient 540


title: P21_S360

description: Mouse non-parenchymal single cells


title: P17_S328

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 2737

value: patient 2737


title: arrayCGH data from patient 2113

value: patient 2113

value: control


title: P12_S288

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 1944

value: patient 1944


title: P10_S272

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 2736

value: patient 2736


title: arrayCGH data from patient 419

value: patient 419


title: P13_S296

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 634

value: patient 634


title: P18_S336

description: Mouse non-parenchymal single cells

value: Liver


title: arrayCGH data from patient 2781

value: patient 2781


title: O4_S32

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 1179

value: patient 1179


title: P15_S312

description: Mouse non-parenchymal single cells


title: O6_S48

description: Mouse non-parenchymal single cells


title: O7_S56

description: Mouse non-parenchymal single cells


title: O2_S16

description: Mouse non-parenchymal single cells


title: O23_S184

description: Mouse non-parenchymal single cells


title: O24_S192

description: Mouse non-parenchymal single cells


title: O1_S8

description: Mouse non-parenchymal single cells


title: O22_S176

description: Mouse non-parenchymal single cells


title: O17_S136

description: Mouse non-parenchymal single cells


title: P11_S280

description: Mouse non-parenchymal single cells


title: O19_S152

description: Mouse non-parenchymal single cells


title: O18_S144

description: Mouse non-parenchymal single cells


title: O15_S120

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 720

value: patient 720


title: O16_S128

description: Mouse non-parenchymal single cells


title: O8_S64

description: Mouse non-parenchymal single cells


title: O13_S104

description: Mouse non-parenchymal single cells


title: O10_S80

description: Mouse non-parenchymal single cells


title: O11_S88

description: Mouse non-parenchymal single cells


title: N9_S263

description: Mouse non-parenchymal single cells


title: N5_S231

description: Mouse non-parenchymal single cells


title: N3_S215

description: Mouse non-parenchymal single cells


title: N4_S223

description: Mouse non-parenchymal single cells


title: N6_S239

description: Mouse non-parenchymal single cells


title: N2_S207

description: Mouse non-parenchymal single cells


title: N21_S359

description: Mouse non-parenchymal single cells


title: O21_S168

description: Mouse non-parenchymal single cells


title: O20_S160

description: Mouse non-parenchymal single cells


title: N23_S375

description: Mouse non-parenchymal single cells


title: N1_S199

description: Mouse non-parenchymal single cells


title: N16_S319

description: Mouse non-parenchymal single cells


title: N22_S367

description: Mouse non-parenchymal single cells


title: N15_S311

description: Mouse non-parenchymal single cells


title: O14_S112

description: Mouse non-parenchymal single cells


title: N19_S343

description: Mouse non-parenchymal single cells


title: N13_S295

description: Mouse non-parenchymal single cells


title: N17_S327

description: Mouse non-parenchymal single cells


title: M8_S63

description: Mouse non-parenchymal single cells


title: N11_S279

description: Mouse non-parenchymal single cells


title: M7_S55

description: Mouse non-parenchymal single cells


title: N14_S303

description: Mouse non-parenchymal single cells


title: M5_S39

description: Mouse non-parenchymal single cells


title: M4_S31

description: Mouse non-parenchymal single cells


title: M3_S23

description: Mouse non-parenchymal single cells


title: M22_S175

description: Mouse non-parenchymal single cells


title: M20_S159

description: Mouse non-parenchymal single cells


title: N24_S383

description: Mouse non-parenchymal single cells


title: M21_S167

description: Mouse non-parenchymal single cells


title: M1_S7

description: Mouse non-parenchymal single cells


title: M23_S183

description: Mouse non-parenchymal single cells


title: M2_S15

description: Mouse non-parenchymal single cells


title: M19_S151

description: Mouse non-parenchymal single cells


title: N20_S351

description: Mouse non-parenchymal single cells


title: M15_S119

description: Mouse non-parenchymal single cells


title: M18_S143

description: Mouse non-parenchymal single cells


title: M11_S87

description: Mouse non-parenchymal single cells


title: M17_S135

description: Mouse non-parenchymal single cells


title: M10_S79

description: Mouse non-parenchymal single cells


title: M12_S95

description: Mouse non-parenchymal single cells


title: L4_S222

description: Mouse non-parenchymal single cells


title: N12_S287

description: Mouse non-parenchymal single cells


title: L5_S230

description: Mouse non-parenchymal single cells


title: L9_S262

description: Mouse non-parenchymal single cells


title: L6_S238

description: Mouse non-parenchymal single cells


title: L8_S254

description: Mouse non-parenchymal single cells


title: M9_S71

description: Mouse non-parenchymal single cells


title: L23_S374

description: Mouse non-parenchymal single cells


title: L3_S214

description: Mouse non-parenchymal single cells


title: L24_S382

description: Mouse non-parenchymal single cells


title: L20_S350

description: Mouse non-parenchymal single cells


title: L22_S366

description: Mouse non-parenchymal single cells


title: L2_S206

description: Mouse non-parenchymal single cells


title: L18_S334

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 2844

value: patient 2844


title: L15_S310

description: Mouse non-parenchymal single cells


title: L14_S302

description: Mouse non-parenchymal single cells


title: L1_S198

description: Mouse non-parenchymal single cells


title: M16_S127

description: Mouse non-parenchymal single cells


title: L21_S358

description: Mouse non-parenchymal single cells


title: L17_S326

description: Mouse non-parenchymal single cells


title: L16_S318

description: Mouse non-parenchymal single cells


title: M13_S103

description: Mouse non-parenchymal single cells


title: K8_S62

description: Mouse non-parenchymal single cells


title: L13_S294

description: Mouse non-parenchymal single cells


title: L11_S278

description: Mouse non-parenchymal single cells


title: L12_S286

description: Mouse non-parenchymal single cells


title: L7_S246

description: Mouse non-parenchymal single cells


title: O3_S24

description: Mouse non-parenchymal single cells


title: K6_S46

description: Mouse non-parenchymal single cells


title: K3_S22

description: Mouse non-parenchymal single cells


title: K9_S70

description: Mouse non-parenchymal single cells


title: K7_S54

description: Mouse non-parenchymal single cells


title: K4_S30

description: Mouse non-parenchymal single cells


title: K21_S166

description: Mouse non-parenchymal single cells


title: K23_S182

description: Mouse non-parenchymal single cells


title: K22_S174

description: Mouse non-parenchymal single cells


title: K20_S158

description: Mouse non-parenchymal single cells


title: K19_S150

description: Mouse non-parenchymal single cells


title: K1_S6

description: Mouse non-parenchymal single cells


title: K17_S134

description: Mouse non-parenchymal single cells


title: K16_S126

description: Mouse non-parenchymal single cells


title: K11_S86

description: Mouse non-parenchymal single cells


title: K14_S110

description: Mouse non-parenchymal single cells


title: K13_S102

description: Mouse non-parenchymal single cells


title: K12_S94

description: Mouse non-parenchymal single cells


title: K15_S118

description: Mouse non-parenchymal single cells


title: K5_S38

description: Mouse non-parenchymal single cells


title: J4_S221

description: Mouse non-parenchymal single cells


title: J23_S373

description: Mouse non-parenchymal single cells


title: J5_S229

description: Mouse non-parenchymal single cells


title: J24_S381

description: Mouse non-parenchymal single cells


title: J2_S205

description: Mouse non-parenchymal single cells


title: J7_S245

description: Mouse non-parenchymal single cells


title: J22_S365

description: Mouse non-parenchymal single cells


title: J3_S213

description: Mouse non-parenchymal single cells


title: J17_S325

description: Mouse non-parenchymal single cells


title: J20_S349

description: Mouse non-parenchymal single cells


title: I9_S69

description: Mouse non-parenchymal single cells


title: K24_S190

description: Mouse non-parenchymal single cells


title: J13_S293

description: Mouse non-parenchymal single cells


title: J6_S237

description: Mouse non-parenchymal single cells


title: K18_S142

description: Mouse non-parenchymal single cells


title: J12_S285

description: Mouse non-parenchymal single cells


title: J15_S309

description: Mouse non-parenchymal single cells


title: I8_S61

description: Mouse non-parenchymal single cells


title: I7_S53

description: Mouse non-parenchymal single cells


title: I5_S37

description: Mouse non-parenchymal single cells


title: I4_S29

description: Mouse non-parenchymal single cells


title: I6_S45

description: Mouse non-parenchymal single cells


title: I3_S21

description: Mouse non-parenchymal single cells


title: I2_S13

description: Mouse non-parenchymal single cells


title: I23_S181

description: Mouse non-parenchymal single cells


title: I24_S189

description: Mouse non-parenchymal single cells


title: I20_S157

description: Mouse non-parenchymal single cells


title: J1_S197

description: Mouse non-parenchymal single cells


title: I18_S141

description: Mouse non-parenchymal single cells


title: I17_S133

description: Mouse non-parenchymal single cells


title: I19_S149

description: Mouse non-parenchymal single cells


title: I15_S117

description: Mouse non-parenchymal single cells


title: I16_S125

description: Mouse non-parenchymal single cells


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