title: BDL

city: Amsterdam

first: Wu

address: B7, Plesmanlaan 121 1066CX Amsterdam

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Raw fastq read files are processed by cell ranger (v3), the output files were uploaded as processed data files.
Analysis were done by R/Bioconductor. Briefly, three samples were first imported and merged into one Seurat3 object. The batch effect was eliminated with fastMNN. Each cell was assigned to a specific cell type unless multiple marker genes were found. The HSC sub-population was extracted and trajectory inference was done using slingshot. Other statistics and plots were mainly performed by Seurat or related R/Bioconductor packages.
Genome_build: GRCm38
Supplementary_files_format_and_content: cell ranger output files. seurat.rds and hsc.rds files are the merged Seurat3 R objects which contain cell type and pseudotime trajectory information.

source_name: Liver

extract_protocol: the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3

treatment_protocol: Corn oil, CCL4, BDL

tag: agent

value: Bile duct ligation

tag: drug

value: Liver


title: dDSB Spo11-myc18 rad50S t6 replicate 1 WCE

status: Public on Jun 09 2021

type: SRA

city: Vienna

first: Franz

last: Klein

address: Dr. Bohr-Gasse 9

department: Chromosome Biology

country: Austria

institute: Max Perutz Labs, University of Vienna

library_source: genomic

data_processing:
library strategy: Protec-seq
Unaligned bam files were converted to fastq files with the help of SamToFastq.jar (picard-tools v1.119). Adapter sequences were trimmed by cutadapt (version 1.8.1) with a maximum error rate of 0.15 and minimum clipped read length of 15 nt (options -O 1 -e 0.15 -m 15 --max-n 3). Clipped read pairs were aligned with the help of NextGenMap (version 0.5.5) to both ASMv1 and the calibration genome ZP591 in order to obtain specific S. cer. and S. kud. alignments, as well as read counts for both the ChIP and the WCE samples. Reads aligning to both genomes, typically only 0.2% of the clipped reads, were discarded. In order to map the 5-prime ends accurately and sensitively, global (end-to-end) alignments, a maximum error rate of 4%, and a kmer-size of 9 were applied. In addition, a maximal insert size of 1000nt was set (upper limit of Illumina sequencing machines), and multiple hits were discarded.
Calibration factors (see supplementary file) were calculated by multiplication of the occupancy ratio (OR), IP.asmv1 x WCE.zp591 / IP.zp591 x WCE.asmv1, with the read count normalization factor (to 10M, RP10M), 10M/IP.asmv1. Conversion of alignment data to various data formats representing dDSB fragments or their 5-prime ends were performed with custom Java scripts. dDSB fragment lengths were determined by the distance between start and ends of read pairs (see fd files). Since these fragments include the 2 nt overhangs generated by the Spo11 staggered cuts at both ends, the cleavage axis distances are obtained by subtracting 2 nt from the respective original fragment lengths.
Wiggle files were created with the help of IGVTools v. 2.3.72.
Genome_build: ASM205788v1 (GenBank accession GCA_002057885.1; "ASMv1") for S. cer.; ZP591 (GenBank accession GCA_000167075.2) for S. kud.
Supplementary_files_format_and_content: For each Protec-Seq IP sample, wiggle files of dDSB fragment 5-prime ends are provided as gz-compressed file archives containing one file each for Watson and Crick (numbers preceding the .wig file extension correspond to the RGB color code). Likewise, fragment depth (fd) files containing chromosome, start, length and depth of each dDSB fragment are listed.

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Saccharomyces kudriavzevii

source_name: meiotic yeast cells

growth_protocol: Diploid SK1 strains were induced to undergo meiosis synchronously and were sampled at desired time points in sporulation medium. Diploid SK1 yeast strains from a frozen stock were grown on YPD plates for 2 days at 30°C. Single colonies were inoculated in 5ml YPD and grown over night at 30°C. For synchronous sporulation, the saturated YPD cultures were inoculated in SPS pre-sporulation medium (0.5% Yeast extract, 1% Peptone, 0.17% Yeast nitrogen base (without amino acids and without ammonium sulfate), 1% potassium acetate, 1% ammonium sulfate, 0.05 M potassium biphtalate, pH 5.5) and grown, shaking vigorously, to an OD660 of 1.0 (4x10^7cells/ml). Cells were harvested by centrifugation, washed once and resuspended in sporulation medium (SPM, 2% potassium acetate, 0.1% polypropylene glycol). The meiotic progression of the cells was monitored by DAPI staining and/or western blot analysis.

extract_protocol:
At the desired time points, cells were harvested from 100 ml meiotic cultures and collected by centrifugation (4 min, 2,000 rpm , 4°C), washed once with ice-cold 1xTBS, centrifuged again and pellets were frozen at -80°C. Cells pellets were lysed in 2.4 ml ice-cold lysis buffer (50 mM Hepes-KOH pH=7.5, 150 mM NaCl, 5 mM EDTA, 1% Trition X-100, 0.1% Na-deoxycholate, 1 protease inhibitor tablet (Roche, Complete Protease Inhibitor Cocktail)). For spike-in experiments, 20-30 % of S. kud. meiotic cells were added to S. cer. cells. All steps were carried out at 4°C unless stated. Cells were opened with glass beads 2 x 20 sec, 5.5 m/s in a FastPrep-24™ 5G Instrument (MP Biomedicals). The cell lysates were centrifuged at full speed for 10 min at 4°C and the supernatants were transferred into new Eppendorf tubes. A pre-clearing step was performed by incubating the soluble chromatin fractions with Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) for 1 hour at 4°C. After removing 40 µl of the lysate for the whole cell extract (WCE), chromatin immunoprecipitation was carried out by incubating the lysates with Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) coupled to anti-myc antibody (9E11, mouse monoclonal AB) for 3 hours at 4°C. Thereafter, the beads were washed 2 times with 1 ml lysis buffer, 2 times with 1 ml lysis buffer high salt, 3 times with 1 ml washing buffer (10 mM Tris-HCL pH=8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 5 mM EDTA) and finally 2 times with 1 ml 10 mM Tris-HCl pH=8.0. Unprotected DNA or partially protected DNA was digested with 3 µl ExonucleaseV (NEB) in NebBuffer 4 (50 mM K-acetate, 20 mM Tris-acetate, 10 mM Mg-acetate and 1 mM DTT at pH=7.9 containing 1 mM ATP) for 30 min at 37°C. In parallel, RNA was removed by incubation with 10 µl RNase (Dnase-free, Roche). The reaction was stopped by the addition of 11 mM EDTA, the beads were washed 3 times with ice-cold 1xTE and incubated at 65°C for 30min in elution buffer (50 mM Tris-HCL pH=8.0, 10 mM EDTA, 1 % SDS). Spo11-protected DNA complexes were digested over night using 12 µl Proteinase K (Sigma) at 50°C. DNA was extracted once with phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 0.5 μg/μl glycogen (Roche), 200 mM NaCl and 2.5 volumes of 96 % ethanol. The DNA was pelleted by centrifugation at 4°C for 1 hour, washed once with 1 ml of 70% ethanol and centrifuged again. After air-drying the pellet for 5 min, the DNA was resuspended in 60 µl 10 mM Tris-Cl pH=8.0. The WCE control was digested with RNase and proteinase K, followed by DNA extraction exactly as with the immunoprecipitated samples.
The immunoprecipitated DNA was digested with 3 µl hTdp2 (BPS Bioscience) in 1x hTdp2 Buffer (50 mM Tris-HCl pH7.4, 1 mM MgCl2, 50 mM KCl, 1 mM DTT, 0.1 mg/ml BSA) at 25°C for 30 min. The DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated as described above. The hTdp2 digested DNA was end-repaired, A-tailed and adapters were ligated to the DNA ends using the NEBNext Ultra II DNA Library Preparation Kit (NEB) according to the manufacturer´s instructions except that we aimed to select for fragments between 140 bp  - 1000 bp length using Agencourt AMPure XP beads (Beckman Coulter). This necessary step likely results in under-representation of the shortest inserts. For amplification, we used either the NEBNext multiplex oligos or the NEBNext dual indexes primer sets. Before library preparation of the WCE control, we fragmented the DNA using NEBNext dsDNA fragmentase (NEB) according to the manufacturer´s protocol. Briefly, we incubated 32µl of the WCE control in 1x fragmentase reaction buffer V2 (50 mM NaCl, 20 mM Tris-HCl, 0.1 mg/ml BSA, 0.15% Triton® X-100, 15 mM MgCl2, pH 7.5@25°C) with 4µl NEBNext dsDNA fragmentase at 37°C for 20 min. The reaction was stopped by the addition of 5 µl of 0.5 M EDTA and the DNA was extracted by phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated as described above. The library preparation of the WCE control was performed the same way as for the immunoprecipitated samples. The concentration and the molarity of the library were determined by NanoDrop™ 3300 Fluorospectrometer and Agilent 2100 Bioanalyzer.

tag: strain

tag: antibody

tag: index 1

value: CGCTCATT

tag: index 2

value: CCTATCCT


title: HA1Q+SA2Q_empty_1

city: Heidelberg

first: F. Nina

last: Papavasiliou

address: Im Neuenheimer Feld 280

department: Tumor Immunology Unit

country: Germany

institute: German Cancer Research Center (DKFZ)

library_source: transcriptomic

data_processing:
RNA-seq raw data from different lanes that belong to the same sample were pulled together. After adapter trimming with Trim Galore (v. 0.6.4; http://www.bioinformatics.babraham.ac.uk/projects/  trim_galore/ ), the trimmed reads were aligned using STAR (v. 2.7.3a) to a genome index inferred by the human reference genome (hg19) sequence, along with the RefSeq annotation, both publicly available at the genome browser at UCSC. For the alignments we considered reads that were uniquely mapped (STAR option: --outFilterMultimapNmax  1) to avoid multimapping between highly similar regions.
Aligned data (bam files) were deduplicated, sorted and indexed with SAMtools (v. 1.9; http://samtools.sourceforge.net).
SNVs in our samples were called with REDItools (v2; https://github.com/tflati/reditools2.0), considering the developers’ recommendations for data preparation prior to this step. Sticking to our previously published approach, we considered only high-quality sites (min. MeanQ > 30 in REDItools2), and we called editing in well-covered sites (min. 50 reads in aggregate of the two replicates per sample) that showed ≥ 10% editing frequency when compared to the control.
Fisher’s exact tests were performed for all the sites that fulfilled the aforementioned criteria and significantly differentially edited sites were considered those that showed adjusted p-value < 0.01.
Sites that were reported in the first 6 sites of a read, or in homopolymeric regions, or reported in the dbSNP (v. 142; excluding cDNA-based reported SNPs: http://www.ncbi.nlm.nih.gov/SNP/), were excluded throughout our output lists.
All genomic coordinates were annotated with Oncotator (v1.9.9.0) and Repeat Mask for Alu-SINE elements of UCSC Genome Browser both for hg19.
Genome_build: hg19
Supplementary_files_format_and_content: allSamples_readcounts.txt: tab-delimited text file includes raw read-counts for all samples sample
Supplementary_files_format_and_content: AGsignal_empty_vs_gRNA.oncoOut.txt: tab-delimited txt file with all A-to-G editing sites with annotated coordinates after variant calling from comparison between the sample 1 and sample 2 (empty samples / reference level) vs sample 3 and sample 4 (gRNA samples).

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: 293 Flp-In T-REx HALO-ADAR1Q + SNAP-ADAR2Q cells were cultivated in Dulbecco’s Modified Eagle Medium (Life Technologies) supplemented with 10 % fetal bovine serum (Life Technologies), 15 µg/ml blasticidin and 100 µg/ml hygromycin (DMEM/FBS/B/H) at 37 °C with 5 % CO2 in a water saturated steam atmosphere.

extract_protocol:
RNA isolation was performed with the RNeasy MinElute Cleanup Kit from Qiagen, followed by DNase I digestion, which was again purified via RNeasy MinElute Cleanup Kit from Qiagen.
The library was prepared with the library preparation kit TruSeq Stranded mRNA by Illumina starting from 100 ng RNA. Samples were then sequenced on a NovaSeq 6000 by ILLUMINA with 50 million reads and 2 × 100 bp paired end.

treatment_protocol: 2⋅106 293 Flp-In T-REx HALO-ADAR1Q + SNAP-ADAR2Q cells were seeded in 2.5 ml DMEM/FBS/B/H supplemented with 10 ng/ml doxycycline in a 6 well plate. After 24 h, 8⋅104 cells per well were reverse transfected in 5 wells of a 96 well plate per sample. For the duplicate of the empty transfection, the cells were treated with an empty reverse transfection with 0.5 µl Lipofectamine 2000 only. For the duplicate of the guideRNA transfection, cells were reverse transfected with 0.5 pmol (snap)2-CAG and 0.5 pmol (halo)2-CAU with 0.5 µl Lipofectamine 2000. Doxycycline concentration was kept at 10 ng/ml and after further 24 h cells were harvested.

tag: cell type

value: 293 Flp-In T-REx

tag: genotype

value: HALO-ADAR1Q + SNAP-ADAR2Q

tag: treatment

value: empty transfection with Lipofectamine 2000


title: CCL4

last: Yang

molecule: total RNA

organism: Mus musculus


title: dDSB Spo11-myc18 rad50S t6 replicate 1 ChIP

value: anti-myc (9E11, mouse monoclonal) antibody

value: ATTACTCG

value: GTACTGAC


title: Oil

value: Corn oil


title: FIL_RNA-4 (Filament cells, biological replicate 4)

status: Public on Jun 08 2021

city: Düsseldorf

first: Michael

last: Feldbrügge

address: Universtitätstr. 1

department: Biology

institute: Heinrich-Heine University Düsseldorf

data_processing:
Base-calling with Illumina RTA 1.18.54.4
Paired-end merging with BBMerge (v 2019) mininsert=24 mininsert0=24 minoverlap=6 minoverlap0=6 ecct extend2=20 iterations=5
Alignment to reference with Hisat2 (v 2.1.0) --dta --no-softclip --known-splicesite-infile
Read count correction for degraded samples with DegNorm (v 0.1.4) default
differential expression analysis using the DegNorm corrected counts with DESeq2 (v 1.32.0) lfcShrink
Genome_build: Umaydis521_2.0, ENSEMBL
Supplementary_files_format_and_content: DegNorm corrected count matrix CSV file, columns = samples, rows = genes
Supplementary_files_format_and_content: DESeq2 results CSV file, rows = genes, columns = see header

organism: Mycosarcoma maydis

source_name: AB33 induced filaments

growth_protocol: Initial sporidial cultures of strain AB33 from Brachmann et al. (2001) were grown to OD600 1.0 ± 0.1 in complete medium according to Holliday (1974), supplemented with 1% glucose (w/v). The cells were shifted to nitrate minimal medium with 2% glucose to induce filamentation. All cultures were grown at 28 degrees Celsius with shaking at 200 rpm. Cells were harvested and EVs isolated from the culture supernatant at 15-16 hours post induction.

extract_protocol:
Cells and EVs were snap frozen and stored at -80 degrees Celsius until extraction. RNA was extracted from EVs and filament samples using standard methods for TRI-reagen LS (Sigma) and TRI-reagent (Sigma), respectively. Extracted RNA was treated with DNase I (ThermoFisher) and re-extracted with TRI-reagent LS. Coprecipitant GlycoBlueTM (ThermoFisher) was used for EV RNA samples for the first extraction and for all samples in the re-extraction.
Libraries for sequencing were generated with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina together with NEBNext® Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instructions.

treatment_protocol: For each replicate, EVs from approximately 300ml of culture supernatant were treated with either 0.1 µg/µl RNase A in phosphate buffered saline (PBS) or just PBS for mock treatment at 4 degrees Celsius for 10 minutes.

tag: sample type

value: cells


title: EV_RN-4 (RNase-treated EVs, biological replicate 4)

source_name: AB33 induced filament EVs

value: EVs

value: RNase


title: EV_RN-3 (RNase-treated EVs, biological replicate 3)


title: EV-4 (Mock-treated EVs, biological replicate 4)

value: Mock (PBS)


title: EV-3 (Mock-treated EVs, biological replicate 3)


title: FIL_RNA-1 (Filament cells, biological replicate 1)


title: EV_RN-2 (RNase-treated EVs, biological replicate 2)


title: EV_RN-1 (RNase-treated EVs, biological replicate 1)


title: shNC_2

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --no-discordant --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: Jurkat cells

growth_protocol: Jurkat cells (CL-0129) were obtained from procell (Wuhan, Hubei, China). The cells were cultured at 37 ℃ with 5% CO2 in RPMI-1640 with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin. Plasmid transfection of Jurkat cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.

extract_protocol:
For PBMCs, whole blood was lysed in four volume of RBCs lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 7.4) at room temperature (RT) and erythrocytes were removed by washing with phosphate buffered saline (PBS). Leukocytes thus obtained lysed in TRI reagent (Sigma-Aldrich, St Louis, MO) for RNA isolation as per the manufacturer's protocol. Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agrose gel electrophoresis.
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95 ℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomizedhexamer.

treatment_protocol: Short hairpin RNA (shRNA) clones for gene of interest were designed by online software (BLOCK-iTTM RNAi Designer, Thermo Fisher Scientific, United States). The silence sequence were TTGCCTTGATATGATTGTTGTT. Sense and antisense strands were annealed to be shRNA. Vector pGFP-B-RS was digested by HindⅢ and BamHⅠ at 37 ℃ for 2h~3h. Then enzyme-digested vector was also run on 1.0% agarose gel and purified by Qiagen column kit. A linearized vector DNA digested by HindⅢ and BamHⅠ and insert shRNA were ligase by T4 DNA Ligase（NEB. Plasmids were introduced into Escherichia coli by chemical transformation. Cells were plated onto LB plates containing kanamycin. Plates were then incubated overnight at 37 ℃. Colonies were screened by colony PCR (30 cycles) with universal primers (located on the backbone vector). The interference sequence of shRNA was verified by Sanger sequencing.

tag: tissue

value: cell line

value: negative control


title: EV-2 (Mock-treated EVs, biological replicate 2)


title: HUH7 siNC-rep2

city: Beijing

first: Xuerui

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

data_processing:
clean RNA-seq reads were mapped to human genome(version hg19) via STAR with genecounts method
Genome_build: hg19

source_name: HUH7 cell line

growth_protocol: HUHU7 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were treated with siRNA for 48h, then total RNA was isolated via Trizol reagent.
Firstly, a Ribozero Kit (Epicentre) was used to remove ribosomal RNA. Then RNA seq library was constructed using an NEB Next Ultra Directional RNA Library Prep Kit (NEB). RNA-seq was carried out with Illumina HiSeq X Ten.

treatment_protocol: HUHU7 cells were seeded into 6 hole plate(typically 2 × 105 cells into a hole) and transfected siRNA-LETN, siRNA-NPM1 and siRNA-NC with Lipofectamine RNAiMAX respectively.

value: HUH7 cell line

value: hepatocellular carcinoma cells


title: Mock reovirus

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

country: USA

institute: Vanderbilt University Medical Center

description:
X2924.TT.9
2924-TT-9-GATCAGAT-TCTTTCCC

organism: blank sample

source_name: Mock virions  were collected by aligning gradients containing virions next to mock gradients, marking the expected position of virions onto the mock gradient

growth_protocol: L929 murine fibroblasts (L cells) were maintained in suspension in glass bottles containing a magnetic stir bar or as monolayers in flasks in Joklik’s minimum essential medium (JMEM; US Biological). Baby hamster kidney cells expressing bacteriophage T7 RNA polymerase under the control of a cytomegalovirus promoter (BHK-T7; Komoto et al. 2014) were maintained in Dulbecco’s minimum essential medium (DMEM; Corning) and were treated with 1 mg/mL Geneticin (Gibco) every other passage. All media were supplemented with 5% fetal bovine serum (FBS; Gibco) 2 mM L-glutamine, 100 U/mL penicillin, 100 µg/mL streptomycin (Corning), and 25 ng/mL amphotericin B.

extract_protocol:
Infected cell pellets were thawed, incubated with 0.14% deoxycholate for 30 min on ice, then sonicated in the presence of Vertrel XF to release virus particles from cells. Virions and TC particles were separated by ultracentrifugation at 25,000 × g in a 1.2-1.4 g/cm3 cesium chloride density gradient. Mock virions and TC particles were collected by aligning gradients containing virions and TC particles next to mock gradients, marking the expected position of virions and TC particles onto the mock gradient, aspirating liquid above the expected position, and transferring 250 µL of the gradient from the expected position of virions and TC particles into clean Eppendorf tubes. Mock preparations and complete virus particles and TC particles were collected and dialyzed in virion storage buffer (150 mM NaCl, 15 mM MgCl2, 10 mM Tris-HCl, pH 7.4). Purified reovirus particles were treated with 1 U/µL benzonase (Sigma) for 1 h at 37°C to degrade extra-particle nucleic acids. RNA content was analyzed by Bioanalyzer (Agilent) before libraries were prepared.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), then Illumina-ready libraries were sequenced by 150 base pair paired-end sequencing on the NovaSeq 6000 Sequencing System (Illumina)

treatment_protocol: L cells (2 × 108) in suspension were adsorbed with media (mock), rsT1L or rsT3DIT1L1 reovirus at a multiplicity of ~10 PFU/cell at 37°C for 48 h. Infected cells were pelleted by centrifugation at 3,000 rpm for 10 min prior to resuspension in homogenization buffer (25 mM NaCl, 10 mM Tris-HCl, pH 7.4, 10 mM β-mercaptoethanol) and stored at -80°C.

value: mock virion


title: CTL_9

source_name: Peripheral blood mononuclear cells

value: blood

value: health individual


title: sh7278_2

value: AC007278.2 knockdown


title: HA1Q+SA2Q_empty_2

source_name: 293 Flp-In T-REx HALO-ADAR1Q + SNAP-ADAR2Q

value: 293 Flp-In T-REx

value: HALO-ADAR1Q + SNAP-ADAR2Q

value: empty transfection with Lipofectamine 2000


title: shNC_1


title: HUH7 siNC-rep1


title: FIL_RNA-2 (Filament cells, biological replicate 2)


title: CTL_7


title: sh7278_1


title: SLE_14

value: SLE patient


title: SLE_13


title: FIL_RNA-3 (Filament cells, biological replicate 3)


title: Liver, 2h after injection of Dex (200 µg) in WT mice, replicate 3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: sample taken 2h after injection of Dex (200 µg) in WT mice, replicate 3

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.32; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 90 derived splice sites (--known-splicesite-infile) and strandedness 'R'
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb90.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed file is a count matrix containg the counts for all samples

growth_protocol: Mice ere kept in an air-conditioned, coventional animal house with food and water ad libitum, with a 14 hours light and 10 hours dark day cycle

extract_protocol:
RNA was isolated using the Aurum total RNA mini kit (Biorad) according to the manufacturer’s instructions
Illumina truseq RNA stranded library protocol (for single end sequencing) as per the manufacturers instructions

treatment_protocol: Both WT and KO m4ice were injected with either PBS or 200 µg of DEX, and livers were isolated two hours post injection

value: C57BL/6J mice

value: WT

value: injection of 200 µg Dexamethasone followed by isolation after 2h

value: liver


title: Liver, 2h after injection of PBS (control) in Zbtb32-/- mice, replicate 2

description: sample taken 2h after injection of PBS (control) in Zbtb32-/- mice, replicate 2

value: ROGKO

value: injection of PBS  followed by isolation after 2h


title: Liver, 2h after injection of Dex (200 µg) in WT mice, replicate 2

description: sample taken 2h after injection of Dex (200 µg) in WT mice, replicate 2


title: Liver, 2h after injection of Dex (200 µg) in WT mice, replicate 1

description: sample taken 2h after injection of Dex (200 µg) in WT mice, replicate 1


title: Liver, 2h after injection of Dex (200 µg) in Zbtb32-/- mice, replicate 1

description: sample taken 2h after injection of Dex (200 µg) in Zbtb32-/- mice, replicate 1


title: Liver, 2h after injection of PBS (control) in WT mice, replicate 1

description: sample taken 2h after injection of PBS (control) in WT mice, replicate 1


title: Liver, 2h after injection of PBS (control) in Zbtb32-/- mice, replicate 3

description: sample taken 2h after injection of PBS (control) in Zbtb32-/- mice, replicate 3


title: Liver, 2h after injection of PBS (control) in WT mice, replicate 2

description: sample taken 2h after injection of PBS (control) in WT mice, replicate 2


title: EV-1 (Mock-treated EVs, biological replicate 1)

value: EVs

value: Mock (PBS)


title: GFP+ Hematopoietic Stem Cell_rp2

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

institute: GIBH

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

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

value: Hematopoietic Stem Cells

value: GFP+ cells of Lin-CD34+CD38- HSPCs cultured in vitro for 96h


title: FOS/GFP+ Hematopoietic Stem Cell_rp2

value: FOS/GFP+ cells of Lin-CD34+CD38- HSPCs cultured in vitro for 96h


title: Mock top component

description:
X2924.TT.10
2924-TT-10-TAGCTTAT-TCTTTCCC

source_name: Mock top component particles were collected by aligning gradients containing TC particles next to mock gradients, marking the expected position of TC particles onto the mock gradient

value: mock top component


title: Hematopoietic Stem Cells - FOS/3FLAG

data_processing:
The sequencing reads were mapped to hg19 using bowtie2, and peaks were called by MACS2(Feng et al., 2012) with a threshold of p <10^-5. Gene ontology analysis were performed by clusterProfiler(Yu et al., 2012). The Genome views of FOS binding to specific genes were visualized by Integrative Genomics Viewer (IGV)(Robinson et al., 2011).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bw

extract_protocol:
1 × 105 FOS/GFP+ cells of Lin-CD34+CD38- HSPCs cultured in vitro for 96h were used to generate DNA libraries according to the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, Cat#: TD901) for sequencing NextSeq 500 (Annoroad Gene Technology).
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody

value: Flag(sigma, f1804)


title: Liver, 2h after injection of PBS (control) in Zbtb32-/- mice, replicate 1

description: sample taken 2h after injection of PBS (control) in Zbtb32-/- mice, replicate 1


title: single cell of Hematopoietic Stem Cell 661

description:
barcodes.tsv
genes.tsv

value: Lin-CD34+CD38-CD45RA-CD90+ HSPCs cultured in vitro for 96h


title: single cell of Hematopoietic Stem Cell 660

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 662

description:
barcodes.tsv
genes.tsv


title: Liver, 2h after injection of Dex (200 µg) in Zbtb32-/- mice, replicate 2

description: sample taken 2h after injection of Dex (200 µg) in Zbtb32-/- mice, replicate 2


title: FOS/GFP+ Hematopoietic Stem Cell_rp3


title: single cell of Hematopoietic Stem Cell 658

description:
barcodes.tsv
genes.tsv


title: FOS/GFP+ Hematopoietic Stem Cell_rp1


title: Liver, 2h after injection of PBS (control) in WT mice, replicate 3

description: sample taken 2h after injection of PBS (control) in WT mice, replicate 3


title: single cell of Hematopoietic Stem Cell 659

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 655

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 657

description:
barcodes.tsv
genes.tsv


title: Liver, 2h after injection of Dex (200 µg) in Zbtb32-/- mice, replicate 3

description: sample taken 2h after injection of Dex (200 µg) in Zbtb32-/- mice, replicate 3


title: single cell of Hematopoietic Stem Cell 656

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 653

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 650

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 652

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 654

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 647

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 645

description:
barcodes.tsv
genes.tsv


title: GFP+ Hematopoietic Stem Cell_rp1


title: single cell of Hematopoietic Stem Cell 642

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 651

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 641

description:
barcodes.tsv
genes.tsv


title: GFP+ Hematopoietic Stem Cell_rp3


title: single cell of Hematopoietic Stem Cell 648

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 644

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 649

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 643

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 638

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 639

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 636

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 637

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 646

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 635

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 634

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 632

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 633

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 630

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 627

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 628

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 629

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 625

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 624

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 622

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 621

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 640

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 623

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 620

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 619

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 617

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 614

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 613

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 618

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 612

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 616

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 611

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 609

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 607

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 610

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 608

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 631

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 604

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 606

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 605

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 603

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 626

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 599

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 602

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 601

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 600

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 597

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 598

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 615

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 595

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 594

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 593

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 592

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 591

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 590

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 587

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 585

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 588

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 589

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 586

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 583

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 584

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 582

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 581

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 580

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 578

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 577

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 579

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 574

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 576

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 571

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 572

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 573

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 575

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 570

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 596

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 569

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 567

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 568

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 563

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 565

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 566

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 564

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 562

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 557

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 559

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 554

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 560

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 555

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 556

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 553

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 558

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 561

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 552

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 550

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 551

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 546

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 547

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 548

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 544

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 541

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 540

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 549

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 539

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 538

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 537

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 543

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 533

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 536

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 534

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 535

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 532

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 531

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 529

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 528

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 527

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 530

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 523

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 524

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 526

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 521

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 525

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 519

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 522

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 545

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 520

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 518

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 517

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 542

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 509

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 515

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 510

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 514

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 512

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 516

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 511

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 505

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 508

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 507

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 506

description:
barcodes.tsv
genes.tsv


title: HL20CT3

city: Shijiazhuang

first: Desmond

middle: Onyeka

last: Agwunobi

address: No. 20 Road East 2nd Ring South Yuhua District

institute: Hebei Normal University

data_processing:
Base calling was done using Illumina Cassava 1.8
Clean reads were obtained from raw reads by removing reads with an adaptor, reads with poly-N, and low quality raw reads. Q20 bases (base quality less than 20), GC content, and sequence duplication level of the clean data were calculated.
Transcriptome assembly was accomplished based on all of the clean reads using a TRINITY V2.2.0 (http://trinityrnaseq.sourceforge.net/), with an optimizing k-mer length of 25 (Grabherr et al., 2011, Nature Biotechnology, 29, 644-52.) and all other parameters were set at default values.
Genome_build: FASTA provided on series record
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Haemaphysalis longicornis

source_name: HL

extract_protocol:
Total RNA was isolated from the whole body of H. longicornis tick samples from each group by TRIzolTM Reagent. RNA sequencing libraries were generated from each sample and the sequencing was performed by Biomarker according to the manual of the NEB Next® UltraTM RNA Library Prep Kit (NEB, Ipswich, MA) in Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Adult ticks

tag: physiological state

value: Unfed ticks

value: 20mg/mL citronellal


title: HL20CT2


title: single cell of Hematopoietic Stem Cell 513

description:
barcodes.tsv
genes.tsv


title: HL20CT1


title: HL15CT1

value: 15mg/mL citronellal


title: HL15CT2


title: HL15CC2

value: 15mg/mL C. citratus oil


title: HL15CC3


title: HL15CT3


title: HL20CC1

value: 20mg/mL C. citratus oil


title: HL20CC3


title: HL15CC1


title: HL20CC2


title: HL10CT1

value: 10mg/mL citronellal


title: HL10CT3


title: HL10CT2


title: HL10CC3

value: 10mg/mL C. citratus oil


title: HL_Ctrl3

value: 50% ethanol (control)


title: HL10CC1


title: HL_Ctrl1


title: HL10CC2


title: single cell of Hematopoietic Stem Cell 502

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 491

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 492

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 494

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 483

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 484

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 493

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 498

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 486

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 482

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 501

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 496

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 500

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 495

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 503

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 490

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 489

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 504

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 485

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 499

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 497

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 488

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 487

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 481

description:
barcodes.tsv
genes.tsv


title: HL_Ctrl2


title: single cell of Hematopoietic Stem Cell 480

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 479

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 478

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 475

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 470

description:
barcodes.tsv
genes.tsv

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


title: single cell of Hematopoietic Stem Cell 468

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 474

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 467

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 469

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 473

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 471

description:
barcodes.tsv
genes.tsv


title: Transgenic rabbits fed High cholesterol diet

city: Nanjing

first: Xiaohong

last: jiang

state: Jiangsu

address: Xianlin Road

institute: Nanjing university

data_processing:
Basic analysis mainly included raw data filtering and quality control, reference genome comparison, alignment homogeneity analysis, saturation analysis, sample correlation analysis, expression analysis, and differential gene analysis.
Advanced analyses mainly included KEGG Pathway and GO Enrichments for the differential expressed genes, in which fpkm>=30 and fold change cutoff =1.5.
Genome_build: OryCun2.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Oryctolagus cuniculus

source_name: vascular

extract_protocol:
Total RNA was extracted from the aortic media of the 9-month-old male non-transgenic and transgenic rabbits using the TruSeq RNA Sample Preparation Kit (Illumina, Cat#FC-122-1001) according to the manufacture’s protocol.
Briefly, mRNA was first enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles.

treatment_protocol: Non-transgenic rabbits fed with chow diet were served as the ctrl group, and transgenic or non-transgenic rabbits fed with high cholesterol diet for 20 weeks were the experimental groups. For each group, RNA from 5 rabbits were included and pooled together.

value: JW/CSK

value: aorta media

value: hight cholesterol diet

value: PGC1-alpha (mouse gene) transgenic

tag: age

value: 9 months

tag: Sex

value: male


title: Ctrl rabbits fed Chow diet

value: chow diet

value: control


title: Ctrl rabbits fed High cholesterol diet


title: single cell of Hematopoietic Stem Cell 472

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells

value: Lin-CD34+CD38-CD45RA-CD90+ HSPCs cultured in vitro for 96h


title: single cell of Hematopoietic Stem Cell 476

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 466

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 477

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 465

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 460

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 459

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 458

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 457

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 464

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 463

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 461

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 462

description:
barcodes.tsv
genes.tsv


title: muscle 1month 20%CR

type: RNA

city: bunkyo-ku

first: Kenji

last: Saito

department: Department of Applied Biological Chemistry

country: Japan

institute: The Univeristy of Tokyo

description:
m-1m-20
Rats fed reduced amount of diet.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Array Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Rattus norvegicus

source_name: rat muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: 5-week-old rats were purchased from Japan SLC (Tokyo, Japan).

extract_protocol: Total RNA was prepared using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

value: Wistar

value: Muscle

tag: gender

value: Male

tag: dietary restriction

value: 20% reduction

tag: time

value: 1 month


title: muscle 1month 30%CR

description:
m-1m-30
Rats fed reduced amount of diet.

tag: strain

value: 30% reduction


title: muscle 1month 10%CR

description:
m-1m-10
Rats fed reduced amount of diet.

value: 10% reduction


title: muscle 1month 5%CR

description:
m-1m-5
Rats fed reduced amount of diet.

value: 5% reduction


title: muscle 1month control

description:
m-1m-C
Rats fed control diet.


title: muscle 1week 5%CR

description:
m-1w-5
Rats fed control diet.

value: 1 week


title: single cell of Hematopoietic Stem Cell 456

description:
barcodes.tsv
genes.tsv

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


title: single cell of Hematopoietic Stem Cell 455

description:
barcodes.tsv
genes.tsv


title: muscle 1week 20%CR

description:
m-1w-20
Rats fed reduced amount of diet.


title: single cell of Hematopoietic Stem Cell 454

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 450

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 451

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 453

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 452

description:
barcodes.tsv
genes.tsv


title: brain 1month 20%CR

description:
b-1m-20
Rats fed reduced amount of diet.

source_name: rat brain

value: Brain


title: single cell of Hematopoietic Stem Cell 448

description:
barcodes.tsv
genes.tsv


title: muscle 1week 10%CR

description:
m-1w-10
Rats fed reduced amount of diet.


title: brain 1month 30%CR

description:
b-1m-30
Rats fed reduced amount of diet.


title: brain 1month 5%CR

description:
b-1m-5
Rats fed reduced amount of diet.


title: single cell of Hematopoietic Stem Cell 449

description:
barcodes.tsv
genes.tsv


title: brain 1week 10%CR

description:
b-1w-10
Rats fed reduced amount of diet.


title: brain 1week control

description:
b-1w-C
Rats fed control diet.


title: brain 1month 10%CR

description:
b-1m-10
Rats fed reduced amount of diet.


title: muscle 1week control

description:
m-1w-C
Rats fed reduced amount of diet.


title: muscle 1week 30%CR

description:
m-1w-30
Rats fed reduced amount of diet.


title: brain 1week 20%CR

description:
b-1w-20
Rats fed reduced amount of diet.


title: brain 1month control

description:
b-1m-C
Rats fed control diet.


title: single cell of Hematopoietic Stem Cell 446

description:
barcodes.tsv
genes.tsv


title: brain 1week 5%CR

description:
b-1w-5
Rats fed reduced amount of diet.


title: brain 1week 30%CR

description:
b-1w-30
Rats fed reduced amount of diet.


title: single cell of Hematopoietic Stem Cell 444

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 447

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 445

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 441

description:
barcodes.tsv
genes.tsv


title: BMMs_RANKL_72h_rep6

city: Seoul

first: Myoung Jun

last: Kim

address: 120 Neungdong-ro, Gwangjin-gu

country: South Korea

institute: konkuk university

description: replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: TMM normalization

source_name: Bone marrow derived macrophage

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Bone marrow cells isolated from tibias and femurs of male mice cultured in α-MEM containing 10 % of fetal bovine serum, 1% of 200 mM L-glutamine and 100 units/ml of penicillin-streptomycin. All cells were cultured at 37℃ at humidified incubator with 5% CO2.

extract_protocol: easy-BLUETM Total RNA Extraction Kit and High Capacity cDNA Reverse Transcription Kit were used to extract total RNA and to synthesis cDNA, respectively.

treatment_protocol: The whole bone marrows were cultured in complete α-MEM medium (α-MEM with 10% fetal bovine serum, 2 mM L-glutamine and 100 units/ml penicillin streptomycin for 24 h. Floating cells were cultured in complete α-MEM medium with 30 ng/ml M-CSF for 72 h. After 72 h, the attached cells were cultured in the presence of 30 ng/ml M-CSF and 100 ng/ml RANKL.

value: 5 weeks

value: M-CSF and RANKL

value: Bone marrow derived macrophage


title: single cell of Hematopoietic Stem Cell 440

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 439

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 442

description:
barcodes.tsv
genes.tsv


title: BMMs_RANKL_72h_rep2

description: replicate 2

value: male


title: BMMs_RANKL_72h_rep4

description: replicate 4


title: single cell of Hematopoietic Stem Cell 437

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells


title: single cell of Hematopoietic Stem Cell 438

description:
barcodes.tsv
genes.tsv


title: BMMs_RANKL_72h_rep5

description: replicate 5


title: BMMs_RANKL_48h_rep6

description: replicate 6


title: BMMs_RANKL_48h_rep4

description: replicate 4


title: single cell of Hematopoietic Stem Cell 435

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 436

description:
barcodes.tsv
genes.tsv


title: BMMs_RANKL_48h_rep3

description: replicate 3


title: BMMs_RANKL_48h_rep1

description: replicate 1


title: single cell of Hematopoietic Stem Cell 434

description:
barcodes.tsv
genes.tsv


title: BMMs_RANKL_48h_rep5

description: replicate 5


title: T277HP-C

type: genomic

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

hyb_protocol: Methylation analysis was performed on the Infinium MethylationEPIC BeadChip Kit (Illumina) following the supplier’s recommendations. Briefly, samples were denatured, neutralized and incubated in the Illumina hybridization oven for 20-24 hours at 37°C to uniformly amplify genomic DNA, then enzymatically fragmented. Following the fragmentation step, samples were hybridized to the BeadChip and incubated at 48°C for 16-24 hours in the Illumina hybridization oven. Finally, non-hybridized and unspecific hybridized DNA samples were washed from the BeadChip, and labeled nucleotides were added to extend and stain primers hybridized to the samples.

scan_protocol: The Illumina iScan system (with the iScan Control Software) was used to scan Illumina MethEpic BeadChips.

data_processing: Raw data were analyzed with GenomeStudio software v2011 according to Illumina’s recommendations to generate result files with beta-values.

label: Cy3, Cy5

source_name: Mesothelioma

label_protocol: Labeling is performed during the hybridation process (see below)

extract_protocol: Genomic DNA from tumor samples were extracted using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) according to the manufacturer’s protocol. DNA quantifications were done  by spectrometry on a NanoDrop-1000 (Ozyme, Saint-Cyr-l’Ecole, France). We used agarose gel migration for DNA to ensure the absence of excessive degradation before  methylation analysis.

tag: patient id

tag: tumor sample localisation

value: Costo-diaphragmatic

tag: tumor cellularity dermined by the pathologist

tag: age at diagnostic

tag: patient's cancer history

tag: asbestos exposure

value: Non-exposed

tag: smoking history

value: no

tag: smoking history (number of pack-year)

tag: histology (type)

value: Epitheloid

tag: histology (subtype - secondary growth patterns)

value: solid

tag: grade (nuclear atypia)

tag: grade (who 2021)

value: High

tag: tumor stage  (8th edition staging system)

value: IV

tag: pet scan

tag: type of tumor sample

value: Diagnostic biopsy

tag: chemotherapy prior tumor sample collection

tag: surgical treatment

tag: surgery type

tag: chemotherapy treatment

value: yes

tag: chemotherapy type

value: Cisplatin/Pemetrexed

tag: survival status

value: dead

tag: overall survival (months)


title: T203LE-C

tag: patient id

tag: tumor sample localisation

tag: tumor cellularity dermined by the pathologist

tag: gender

value: Male

tag: age at diagnostic

tag: patient's cancer history

tag: asbestos exposure

value: Exposed

value: papillary

value: IIIB

value: Surgical resection

value: Extended pleurectomy decortication (P/D)


title: BMMs_RANKL_24h_rep6

description: replicate 6

tag: strain

tag: age

value: 5 weeks

tag: Sex

value: male

tag: treatment

value: M-CSF and RANKL

tag: time

tag: cell type

value: Bone marrow derived macrophage


title: BMMs_RANKL_24h_rep5

description: replicate 5


title: BMMs_RANKL_72h_rep3

description: replicate 3


title: T227LE-D

value: Apx (Highest metabolic site detected by PET scan)

tag: smoking history

value: no

tag: smoking history (number of pack-year)

tag: histology (type)

value: Epitheloid

tag: histology (subtype - secondary growth patterns)

value: small cell

tag: grade (nuclear atypia)

tag: grade (who 2021)

tag: tumor stage  (8th edition staging system)

value: IIIA

tag: pet scan

tag: type of tumor sample

tag: chemotherapy prior tumor sample collection

tag: surgical treatment

tag: surgery type

tag: chemotherapy treatment

value: Carboplatin/Pemetrexed


title: single cell of Hematopoietic Stem Cell 429

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells

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


title: BMMs_RANKL_24h_rep3

description: replicate 3

tag: strain

tag: age

tag: Sex


title: single cell of Hematopoietic Stem Cell 430

description:
barcodes.tsv
genes.tsv

tag: cell type

tag: treatment


title: BMMs_RANKL_48h_rep2

description: replicate 2

tag: time


title: T333HP-C

tag: patient id

tag: tumor sample localisation

value: Costo-diaphragmatic

tag: tumor cellularity dermined by the pathologist

tag: gender

value: Female

tag: age at diagnostic

tag: patient's cancer history

tag: asbestos exposure

tag: smoking history

tag: smoking history (number of pack-year)

tag: histology (type)

value: Biphasic

value: trabecular

value: High

value: IV

value: Diagnostic biopsy

tag: chemotherapy type

tag: survival status

value: dead

tag: overall survival (months)


title: single cell of Hematopoietic Stem Cell 433

description:
barcodes.tsv
genes.tsv


title: T278HP-C

value: Breast cancer

value: Non-exposed

value: yes

tag: histology (subtype - secondary growth patterns)

tag: grade (nuclear atypia)

tag: grade (who 2021)

value: Low

tag: tumor stage  (8th edition staging system)

tag: pet scan

tag: type of tumor sample

tag: chemotherapy prior tumor sample collection

tag: surgical treatment

tag: surgery type

tag: chemotherapy treatment


title: single cell of Hematopoietic Stem Cell 431

description:
barcodes.tsv
genes.tsv

tag: cell type

tag: treatment


title: T333HP-A

tag: patient id

tag: tumor sample localisation

value: Apex

tag: tumor cellularity dermined by the pathologist

tag: gender

tag: age at diagnostic

tag: patient's cancer history

tag: asbestos exposure

tag: smoking history

value: no

tag: smoking history (number of pack-year)


title: T227LE-A

value: Male

value: Exposed

tag: histology (type)

value: Epitheloid

tag: histology (subtype - secondary growth patterns)

value: small cell

tag: grade (nuclear atypia)

tag: grade (who 2021)

tag: tumor stage  (8th edition staging system)

value: IIIA

tag: pet scan

value: Surgical resection

value: Extended pleurectomy decortication (P/D)

tag: chemotherapy type

value: Carboplatin/Pemetrexed

tag: survival status

tag: overall survival (months)


title: single cell of Hematopoietic Stem Cell 426

description:
barcodes.tsv
genes.tsv

tag: cell type

value: Hematopoietic Stem Cells

tag: treatment

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


title: single cell of Hematopoietic Stem Cell 425

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 424

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 423

description:
barcodes.tsv
genes.tsv


title: T278HP-A

tag: patient id

tag: tumor sample localisation

tag: tumor cellularity dermined by the pathologist

tag: gender

value: Female

value: trabecular

value: IV

tag: type of tumor sample

value: Diagnostic biopsy

tag: chemotherapy prior tumor sample collection

tag: surgical treatment

tag: surgery type

tag: chemotherapy treatment

value: dead


title: single cell of Hematopoietic Stem Cell 422

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 421

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 443

description:
barcodes.tsv
genes.tsv


title: T277HP-A

value: Apex

tag: age at diagnostic

tag: patient's cancer history

tag: asbestos exposure

value: Non-exposed

tag: smoking history

tag: smoking history (number of pack-year)

tag: histology (type)

tag: histology (subtype - secondary growth patterns)

value: solid

tag: grade (nuclear atypia)

tag: grade (who 2021)

value: High

value: yes

value: Cisplatin/Pemetrexed


title: single cell of Hematopoietic Stem Cell 420

description:
barcodes.tsv
genes.tsv

tag: cell type

tag: treatment


title: single cell of Hematopoietic Stem Cell 432

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 417

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 416

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 428

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 427

description:
barcodes.tsv
genes.tsv


title: BMMs_RANKL_24h_rep4

description: replicate 4

tag: strain

tag: age

value: 5 weeks

tag: Sex

value: male

value: M-CSF and RANKL

tag: time

value: Bone marrow derived macrophage


title: BMMs_RANKL_0h_rep6

description: replicate 6

value: control


title: single cell of Hematopoietic Stem Cell 419

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells

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


title: single cell of Hematopoietic Stem Cell 418

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 413

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 415

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 414

description:
barcodes.tsv
genes.tsv


title: T203LE-A

tag: patient id

tag: tumor sample localisation

tag: tumor cellularity dermined by the pathologist

tag: gender

value: Male

value: Exposed

value: no

value: Epitheloid

value: papillary

tag: tumor stage  (8th edition staging system)

value: IIIB

tag: pet scan

tag: type of tumor sample

value: Surgical resection

tag: chemotherapy prior tumor sample collection

tag: surgical treatment

tag: surgery type

value: Extended pleurectomy decortication (P/D)

tag: chemotherapy type

tag: survival status

tag: overall survival (months)


title: BMMs_RANKL_72h_rep1

description: replicate 1

tag: strain

tag: treatment

tag: cell type


title: single cell of Hematopoietic Stem Cell 412

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 411

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 410

description:
barcodes.tsv
genes.tsv


title: BMMs_RANKL_0h_rep4

description: replicate 4

tag: age

tag: Sex

tag: time


title: TR9 (BM cells from 3 TR9 mice)

city: Tianjin

first: yang

last: xue

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College

data_processing:
Primary sequencing data named raw reads are produced by Illumina HiSeq 2000.
Raw reads are saved as FASTQ file and are filtered into clean reads, and then mapped to genome reference using BWA and Bowtie.
Gene expression levels are quantified by RSEM.
Screening of DEGs between two samples are based on the analysis method of the poisson distribution.
Subsequent enrichment analyses of GO, KEGG and GSEA were performed and visualized using R package clusterprofiler.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample.

source_name: GFP+ bone marrow cells

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype

tag: tissue

value: Bone Marrow

value: GFP+ bone marrow cells


title: single cell of Hematopoietic Stem Cell 409

description:
barcodes.tsv
genes.tsv


title: TR1 (BM cells from 3 TR1 mice)


title: Control (BM cells from 3 wild-type mice)

source_name: Lin- bone marrow cells

value: wild type

value: Lin- bone marrow cells


title: BMMs_RANKL_0h_rep1

description: replicate 1

value: 5 weeks

value: male


title: BMMs_RANKL_0h_rep5

description: replicate 5

value: control

value: Bone marrow derived macrophage


title: Uveal melanoma cell-92.1-3

city: Shanghai

first: AI

last: ZHUANG

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Uveal melanoma patient

growth_protocol: The 92.1 cells were cultured in 1640 supplemented with 10% FBS. The PIG1 cells were cultured in f-12k with 10%FBS.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and 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

treatment_protocol: The cells were digested by trypsin and resuspended with culture medium.

tag: diagnosis/tissue

value: Uveal melanoma

value: uveal melanoma cells


title: BMMs_RANKL_0h_rep3

description: replicate 3


title: Uveal melanoma cell-92.1-2


title: BMMs_RANKL_24h_rep1

description: replicate 1

value: M-CSF and RANKL


title: PDC1-Luc+CAF JQ1

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

data_processing: Illumina GenomeStudio 2010, quantile normalization

source_name: patient derived cancer cells

label_protocol: not provided

growth_protocol: patient-derived cancer cells (PDC) were cultured in DMEM medium (Gibco) supplemented with 10%FBS, NEAA and insulin.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 1μM JQ1,2.5μM pacritinib or combination were used in treatment for 8hr

value: colorectal cancer

tag: culture methed

value: co-cultured with CAFs

tag: drug treatment


title: LSK_Evl_OE_d11_rep2

first: Friederike

last: Herbst

address: INF 460

institute: National Center for Tumor Diseases (NCT) & German Cancer Research Center (DKFZ)

description: Sample 2

hyb_protocol: Standard Illumina Hybridisation Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide).  1,5 ug of cRNA were hybridized for 17 hr at 58°C on Illumina Mouse (WG-6)-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing: Data were normalized using quantile normalization with the Bioconductor package preprocessCore for R.

label: Biotin, Cy3-Streptavidin

source_name: bone marrow

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Life Technologies) was used to generate single-stranded cRNA from input amounts of 200 ng total RNA.

growth_protocol: Cells were cultured in StemSpan supplemented with 100 ng/ml rmSCF, 100 ng/ml rmFlt3 Ligand, 100 ng/ml rhTPO, 20 ng/ml rmIL3 and 1% penicillin/streptomycin at 37°C in a humidified, 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using the ARCTURUS® PicoPure® RNA Isolation Kit according to the manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Cells were lentivirally transduced with a vector encoding for Evl, miR-342 and mock, sorted for fluorescence marker positivity and harvested 11 days post transduction.

value: 6-8 weeks

value: bone marrow

tag: cell population

value: Lineage- Sca1+ cKit+

tag: vector

value: lentivirus

tag: transgene

value: Evl

tag: time point

value: 11 days post transduction


title: PDC1-Luc+CAF pac+JQ1

value: JQ1 and pacritinib


title: LSK_miR-342_OE_d11_rep2

description: Sample 4


title: single cell of Hematopoietic Stem Cell 408

description:
barcodes.tsv
genes.tsv

value: Hematopoietic Stem Cells

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


title: LSK_mock_OE_d11_rep1

description: Sample 5

value: mock


title: LSK_miR-342_OE_d11_rep1

description: Sample 3


title: single cell of Hematopoietic Stem Cell 407

description:
barcodes.tsv
genes.tsv


title: Uveal melanoma cell-92.1-1


title: BMMs_RANKL_0h_rep2

description: replicate 2

value: 5 weeks

value: male

value: control


title: Normal melanocyte-PIG1-3

source_name: Nevus

value: Nevus

value: normal melanocytes


title: LSK_Evl_OE_d11_rep1

description: Sample 1


title: PDC1-Luc mono-culture

value: colorectal cancer

value: mono-cultured


title: BMMs_RANKL_24h_rep2

description: replicate 2

value: M-CSF and RANKL

value: Bone marrow derived macrophage


title: Normal melanocyte-PIG1-2


title: single cell of Hematopoietic Stem Cell 406

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 404

description:
barcodes.tsv
genes.tsv


title: Normal melanocyte-PIG1-1


title: single cell of Hematopoietic Stem Cell 405

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 403

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 400

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 401

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 399

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 402

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 396

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 397

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 398

description:
barcodes.tsv
genes.tsv


title: Mia PaCa2-OE_rep2

first: Yanhong

last: Wang

address: 5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences

description: Mia PaCa2 with LIFR over-expression replicate 2

data_processing:
Paired-end ChIP-seq reads were aligned to GRCh38 genome assembly using Bowtie2 with options ‘--local --very-sensitive-local --no-unal --nomixed --no-discordant --phred33 -I 10 -X 700’ followed by sorting using SAMtools
MACS2 were used to call peaks under parameters “-f BAMPE --keep-dup all”.
In order to normalize sequencing depth for each replicate, bamCompare and bamCovergae from deepTools was used to generate bigWig file based on BAM files
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files
Supplementary_files_format_and_content: peak text files

source_name: pancreatic cancer cells

growth_protocol: Cells were cultured in DMEM (Corning, USA) supplemented with 10% fetal bovine serum (FBS, Hyclone, USA) and 1% antibiotic mixture (Gibco, USA) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Specific DNA fragments were obtained, purified, and subjected to PCR amplification using a NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein Scientific Inc, Cat.No:N259-YH01)
Libraries were prepared according to the a NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein Scientific Inc), according to the protocol of the manufacturer.

treatment_protocol: untreated

value: pancreatic cancer cell

value: Mia PaCa2

tag: chip antibody

value: STAT3 (Cell Signaling Technology, 124H6, lot 9139)

value: LIFR over-expression


title: Mia PaCa2-OE_rep1

description: Mia PaCa2 with LIFR over-expression replicate 1

tag: strain


title: Mia PaCa2-NC_rep3_input

description: Mia PaCa2 untreated replicate3 input DNA

tag: treatment

value: untreated


title: single cell of Hematopoietic Stem Cell 395

description:
barcodes.tsv
genes.tsv

tag: cell type

value: Hematopoietic Stem Cells


title: single cell of Hematopoietic Stem Cell 394

description:
barcodes.tsv
genes.tsv

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


title: Mia PaCa2-OE_rep3

description: Mia PaCa2 with LIFR over-expression replicate 3


title: Mia PaCa2-NC_rep3

description: Mia PaCa2 untreated replicate3


title: single cell of Hematopoietic Stem Cell 393

description:
barcodes.tsv
genes.tsv


title: Mia PaCa2-NC_rep2_input

description: Mia PaCa2 untreated replicate2 input DNA


title: PDC1-Luc+CAF pac

value: co-cultured with CAFs

value: pacritinib


title: LSK_mock_OE_d11_rep2

description: Sample 6

tag: age

value: 6-8 weeks

value: bone marrow

value: Lineage- Sca1+ cKit+

value: lentivirus

value: mock

value: 11 days post transduction


title: single cell of Hematopoietic Stem Cell 392

description:
barcodes.tsv
genes.tsv


title: Mia PaCa2-NC_rep1_input

description: Mia PaCa2 untreated replicate1 input DNA


title: Mia PaCa2-NC_rep1

description: Mia PaCa2 untreated replicate1


title: single cell of Hematopoietic Stem Cell 390

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 389

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 388

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 387

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 384

description:
barcodes.tsv
genes.tsv


title: THP-1_Test_S44

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

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: single cell of Hematopoietic Stem Cell 382

description:
barcodes.tsv
genes.tsv


title: THP-1_Test_S43


title: single cell of Hematopoietic Stem Cell 385

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 383

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 380

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 381

description:
barcodes.tsv
genes.tsv


title: THP-1_Control_S83


title: single cell of Hematopoietic Stem Cell 391

description:
barcodes.tsv
genes.tsv


title: THP-1_Control_S84


title: Mia PaCa2-NC_rep2

description: Mia PaCa2 untreated replicate2


title: single cell of Hematopoietic Stem Cell 379

description:
barcodes.tsv
genes.tsv


title: THP-1_Control_S82


title: THP-1_Test_S86


title: THP-1_Control_S81


title: THP-1_Test_S88


title: single cell of Hematopoietic Stem Cell 377

description:
barcodes.tsv
genes.tsv


title: THP-1_Test_S42


title: THP-1_Control_S40


title: single cell of Hematopoietic Stem Cell 386

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 376

description:
barcodes.tsv
genes.tsv


title: THP-1_Control_S39


title: THP-1_Test_S85


title: single cell of Hematopoietic Stem Cell 375

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 378

description:
barcodes.tsv
genes.tsv


title: THP-1_Control_S38


title: THP-1_Test_S41


title: single cell of Hematopoietic Stem Cell 372

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 373

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 374

description:
barcodes.tsv
genes.tsv


title: FF367A RNA-seq [validation cohort]

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

description:
RNA-362-1-7_30_14_S71
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

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: Female


title: C2D21C RNA-seq [validation cohort]

description:
RNA-361-2-7_1_14_S70
processed data file:
QCed_counts_batch2_allsamples.txt

value: No

value: Male


title: 729A90 RNA-seq [validation cohort]

description:
RNA-363-1-9_5_14_S72
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 370

description:
barcodes.tsv
genes.tsv

source_name: Hematopoietic Stem Cells from Peripheral blood after mobilization

value: Hematopoietic Stem Cells


title: single cell of Hematopoietic Stem Cell 369

description:
barcodes.tsv
genes.tsv

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


title: single cell of Hematopoietic Stem Cell 371

description:
barcodes.tsv
genes.tsv


title: B84332 RNA-seq [validation cohort]

description:
RNA-359-2-4_30_14_S68
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: 195214 RNA-seq [validation cohort]

description:
RNA-358-1-3_5_14_S67
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 367

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 368

description:
barcodes.tsv
genes.tsv


title: CC376C RNA-seq [validation cohort]

description:
RNA-357-1-3_3_14_S66
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 366

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 365

description:
barcodes.tsv
genes.tsv


title: DDF5C0 RNA-seq [validation cohort]

description:
RNA-354-91-2_11_14_S18
processed data file:
QCed_counts_batch2_allsamples.txt


title: 6832F1 RNA-seq [validation cohort]

description:
RNA-354-97-2_19_14_S19
processed data file:
QCed_counts_batch2_allsamples.txt


title: 2C5AB3 RNA-seq [validation cohort]

description:
RNA-354-75-2_6_14_S17
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 364

description:
barcodes.tsv
genes.tsv


title: 768500 RNA-seq [validation cohort]

description:
RNA-354-61-1_31_14_S16
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 362

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 363

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 361

description:
barcodes.tsv
genes.tsv


title: BB3963 RNA-seq [validation cohort]

description:
RNA-354-31-1_24_14_S14
processed data file:
QCed_counts_batch2_allsamples.txt


title: 932A93 RNA-seq [validation cohort]

description:
RNA-354-47-1_29_14_S15
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 360

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 359

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 358

description:
barcodes.tsv
genes.tsv


title: 6941A2 RNA-seq [validation cohort]

description:
RNA-354-2-1_16_14_S12
processed data file:
QCed_counts_batch2_allsamples.txt


title: DD4D91 RNA-seq [validation cohort]

description:
RNA-354-132-3_21_14_S24
processed data file:
QCed_counts_batch2_allsamples.txt


title: 13BC57 RNA-seq [validation cohort]

description:
RNA-354-139-3_28_14_S25
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 354

description:
barcodes.tsv
genes.tsv


title: 6D3106 RNA-seq [validation cohort]

description:
RNA-354-15-1_22_14_S13
processed data file:
QCed_counts_batch2_allsamples.txt


title: 47571C RNA-seq [validation cohort]

description:
RNA-354-125-3_19_14_S23
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 353

description:
barcodes.tsv
genes.tsv


title: A941DB RNA-seq [validation cohort]

description:
RNA-360-1-6_18_14_S69
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 355

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 356

description:
barcodes.tsv
genes.tsv


title: FD6773 RNA-seq [validation cohort]

description:
RNA-354-106-3_2_14_S21
processed data file:
QCed_counts_batch2_allsamples.txt


title: 95C8D0 RNA-seq [validation cohort]

description:
RNA-354-112-3_6_14_S22
processed data file:
QCed_counts_batch2_allsamples.txt


title: 017D12 RNA-seq [validation cohort]

description:
RNA-346-2-11_2_13_S65
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: C4D725 RNA-seq [validation cohort]

description:
RNA-343-2-10_2_13_S64
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 350

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 351

description:
barcodes.tsv
genes.tsv


title: C2BAFF RNA-seq [validation cohort]

description:
RNA-342-64-9_4_13_S28
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 349

description:
barcodes.tsv
genes.tsv


title: 3CDA0F RNA-seq [validation cohort]

description:
RNA-342-3-8_26_13_S63
processed data file:
QCed_counts_batch2_allsamples.txt


title: 19C0BF RNA-seq [validation cohort]

description:
RNA-342-43-8_30_13_S27
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 348

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 347

description:
barcodes.tsv
genes.tsv


title: DC746D RNA-seq [validation cohort]

description:
RNA-342-23-8_28_13_S26
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 346

description:
barcodes.tsv
genes.tsv


title: DFD210 RNA-seq [validation cohort]

description:
RNA-342-157-9_19_13_S49
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 345

description:
barcodes.tsv
genes.tsv


title: F424AF RNA-seq [validation cohort]

description:
RNA-342-141-9_17_13_S31
processed data file:
QCed_counts_batch2_allsamples.txt


title: D85F17 RNA-seq [validation cohort]

description:
RNA-342-105-9_10_13_S29
processed data file:
QCed_counts_batch2_allsamples.txt


title: 4619B8 RNA-seq [validation cohort]

description:
RNA-338-1-7_9_13_S61
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 342

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 340

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 343

description:
barcodes.tsv
genes.tsv


title: F2FD07 RNA-seq [validation cohort]

description:
RNA-339-21-7_18_13_S62
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: DA017C RNA-seq [validation cohort]

description:
RNA-354-101-2_26_14_S20
processed data file:
QCed_counts_batch2_allsamples.txt


title: PDC1-Luc+CAF

tag: tissue

value: colorectal cancer

value: co-cultured with CAFs

value: vehicle


title: single cell of Hematopoietic Stem Cell 341

description:
barcodes.tsv
genes.tsv


title: FD4CD2 RNA-seq [validation cohort]

description:
RNA-336-1-5_14_13_S60
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 339

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 338

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 337

description:
barcodes.tsv
genes.tsv


title: 4C688B RNA-seq [validation cohort]

description:
RNA-335-58-5_23_13_S4
processed data file:
QCed_counts_batch2_allsamples.txt

value: Mixed Candida/bacterial


title: 451FB2 RNA-seq [validation cohort]

description:
RNA-335-97-6_4_13_S6
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 336

description:
barcodes.tsv
genes.tsv


title: 87C4A8 RNA-seq [validation cohort]

description:
RNA-335-42-5_16_13_S3
processed data file:
QCed_counts_batch2_allsamples.txt


title: THP-1_Control_S37


title: BA2178 RNA-seq [validation cohort]

description:
RNA-335-23-5_14_13_S2
processed data file:
QCed_counts_batch2_allsamples.txt


title: 611755 RNA-seq [validation cohort]

description:
RNA-335-157-7_11_13_S11
processed data file:
QCed_counts_batch2_allsamples.txt


title: 957C6C RNA-seq [validation cohort]

description:
RNA-342-122-9_13_13_S30
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 357

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 352

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 344

description:
barcodes.tsv
genes.tsv


title: 450001 RNA-seq [validation cohort]

description:
RNA-335-147-7_4_13_S10
processed data file:
QCed_counts_batch2_allsamples.txt


title: A5DC94 RNA-seq [validation cohort]

description:
RNA-335-138-6_27_13_S9
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 332

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 331

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 329

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 328

description:
barcodes.tsv
genes.tsv


title: D2192B RNA-seq [validation cohort]

description:
RNA-335-_2-5_8_13_S1
processed data file:
QCed_counts_batch2_allsamples.txt


title: B0BD5D RNA-seq [validation cohort]

description:
RNA-335-78-5_30_13_S5
processed data file:
QCed_counts_batch2_allsamples.txt


title: single cell of Hematopoietic Stem Cell 327

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 330

description:
barcodes.tsv
genes.tsv


title: A5813D RNA-seq [validation cohort]

description:
RNA-333-_1-1_21_13_S58
processed data file:

value: Fail


title: single cell of Hematopoietic Stem Cell 326

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 335

description:
barcodes.tsv
genes.tsv


title: CAC382 RNA-seq [validation cohort]

description:
RNA-312-_1-1_31_12_S57
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 334

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 333

description:
barcodes.tsv
genes.tsv


title: single cell of Hematopoietic Stem Cell 324

description:
barcodes.tsv
genes.tsv