title: WT-Bone Marrow , input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Trim_galore, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the mm10 genome using HISAT2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
The specific peaks  were merged by bedtools,and calculate the peak read by bedtools coverage.
Assembly: Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

source_name: Bone Marrow

extract_protocol:
3 million cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using ultrasonicator (Bioruptor).
Libraries were amplified using 20 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length.

value: Mouse Bone Marrow


title: 3d7d_SS2_146814.46d [SLX-19981.i726_i513]

status: Public on Jun 20 2023

type: SRA

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX19981_SLX19982_scB5Tom_3d7d_ss2_fcounts.txt

library_source: transcriptomic single cell

data_processing:
library strategy: Smart-Seq2 or 10x Genomics
Smart-Seq2 sequencing reads were aligned to the mouse genome (mm10) using the STAR aligner (version 2.7.3a) with default parameters. Reads mapping to exons were counted with featureCounts (version 2.0.0) using the ENSEMBL v93 annotation. For consistency only a single read was processed for each sample. 10x genomics reads were pre-processed using cellranger (version 3.1.0, reference genome and annotation version 3.0.0) with default settings
Assembly: mm10
Supplementary files format and content: Smart-Seq2 data: count matrices for each fastq file as produced by feature counts  10x Genomics data: annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
All steps in this section (unless otherwise indicated) were performed on ice, and centrifugation steps performed at 300g, 4°C for 5 min. 8-12 weeks old mice carrying the Hoxb5-Cre and the Rosa26-LoxP-STOP-LoxP-tdTomato constructs were treated with 7 daily injections of tamoxifen and sacrificed at indicated time points. Bone marrow cells were extracted from ilia, tibiae and femura by grinding with mortar and pestle in PBS supplemented with 2% Fetal Bovine Serum (cell buffer). The suspension was filtered through a 50µm filter, centrifuged and resuspended in 3 ml of cell buffer. Red blood cells were removed using the ammonium chloride solution: 5 ml of 0.8% Ammonium Chloride (StemCell Tech. 07800) was added to the suspension and incubated for 10 min with intermittent mixing. Afterwards cells were diluted with 7 ml of cell buffer, centrifuged and resuspended in 1 ml of cell buffer. Subsequently, lineage depletion was performed as follows: added 20 µl of the EasySep mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), incubated for 15 min, added 30 µl magnetic particles, incubated for 10 min, added 1.5 ml of cell buffer and placed tubes in a magnet, incubated for 3 min at room temperature and eluted cells twice (with additional 2.5 ml of cell buffer). Afterwards, cells were centrifuged, resuspended in 200 µl of cell buffer and stained with the antibody panel as follows: antibody mix was added, cells were incubated for 30 min, washed with 2 ml of cell buffer, centrifuged, reuspended in 200 µl cell buffer. For the secondary staining Streptavidin-BV510 was added, cells were washed with 2 ml of cell buffer, centrifuged and resuspended in 1000 µl of cell buffer supplemented with 7AAD. Afterwards cells were sorted with BD influx sorter into either 96 well plates containing 2.3 µl lysis buffer (for the Smart-Seq2 protocol) or 100 µl of PBS with 0.04% BSA in eppendorf tubes ('droplet buffer') when used for the 10x Genomics scRNA-Seq protocol. The Smart-Seq2 plates were vortexed, centrifuged at 800g for 2 min and stored at -80°C. Antibodies and fluorochromes used: Mouse haematopoietic progenitor cell isolation cocktail (Stem Cell Technologies 19856), CD48-APC (Thermo-Fischer 17-0481-82), c-Kit-APC/Cy7 (Biolegend 105826), Sca1-BV421 (Biolegend 108133) and CD150-PE/Cy7 (Biolegend 115914), Streptavidin-BV510 (Biolegend 405234), 7AAD (Thermo Fischer A1310).
Smart-Seq2:
When cell numbers were limiting single cells were profiled with a modified version of the Smart-Seq2 protocol rather than 10x Genomics kit. Single cells were sorted into 96-well plates with 2.3 µl lysis buffer containing 0.115 µl of SUPERase-In RNase Inhibitor at 20 U/µl concentration (ThermoFisher AM2694) and 0.23 µl of 10% Triton X-100 solution (Sigma 93443), plates were vortexed and stored at -80°C. After thawing 2 µl of the annealing solution (0.1 µl of ERCC RNA Spike-In solution (1:300,000 dilution) Thermo-Fisher 4456740), 0.02 µl of the oligo-dT primer (100 µM stock concentration) and 1 µl of dNTP (10 mM stock concentration)) was added. The plate was incubated at 72°C for 3 min, cooled down on ice and reverse transcription was performed by adding 5.7 µl of RT buffer (0.1 µl of Maxima H minus reverse transcriptase at 200 U/µl concentration (ThermoFischer EP0752), 0.25 µl of SUPERase-In RNAse Inhibitor at 20 U/µl concentration, 2 µl of the Maxima enzyme buffer, 0.2 µl of TSO oligo at 100 µM concentration, 1.875 µl of PEG 8000 solution (Sigma P1458) at 40% v/v concentration and 1.275 µl water) and incubation at 42°C for 90 min followed by incubation at 70°C for 15 min. Immediately after, cDNA was amplified by PCR by adding 1 µl of the Terra PCR Direct Polymerase (1.25 U/µl, Takara 639270), 25 µl of the Terra PCR Direct buffer and 1 µl of the ISPCR primer (10 µM stock concentration) to a total volume of 50 µl using the following PCR conditions: 98°C for 3 min, 98°C for 15 s, 65°C for 30 s, 68°C for 4 min (21 cycles), 72°C for 10 min. The amplified cDNA was purified using AMPure XP beads (Beckman A63882), quantified using the PicoGreen assay (ThermoFischer P7589) and used for Nextera library preparation. The libraries were generated using either a standard protocol (batch 7d) or modified protocol (batches 3d7d, 2w4w and 3dr2), see the corresponding metadata) described below. No obvious batch effects were observed among cells analysed with either of the protocols.
The standard Nextera protocol: cDNA was diluted to approximately 50-150 pg/µl and 1.25 µl of the solution was used, 2.5 µl of Tagment DNA buffer 1.25 µl of Amplicon Tagment Mix (Nextera XT kit, Illumina FC-131-1096) were added, samples were incubated at 55°C for 10 min, and the reaction was stopped by addition of 1.25 µl of NT buffer. Tagmentation products were amplified by PCR by adding 1.25 µl of each N and S primers (Illumina Nextera XT 96-index kit FC-131-1002) and 3.75 µl of NPM solution and using the following thermocycler settings: 72°C 3 min, 95°C 30 s, 12 cycles of 95°C 30s, 55°C 30s, 72°C 60s and a final extension at 72°C for 5 min.
The modified Nextera protocol follows the same principle as the standard Nextera protocol and includes the following steps: cDNA was diluted to approximately 50-150 pg/µl and 1.03 µl of the solution was used, 1.63 µl of Tagment DNA buffer and 0.6 µl Amplicon Tagment Mix was added, samples were incubated at 55°C for 10 min, the reaction was stopped by adding 0.82 µl of NT buffer. Tagmentation products were amplified by adding 1.23 µl of each N and S primers (as above but diluted 5 times), 2.3 µl of Phusion HF buffer (ThermoFischer F530L), 0.1 µl of dNTP (25 mM stock concentration), 0.07 µl of Phusion polymerase and 2.5 µl of water and using the following thermocycler settings: 72°C 3 min, 98°C 3 min s, 12 cycles of 98°C 10s, 55°C 30s, 72°C 30s and a final extension at 72°C for 5 min.
Libraries were sequenced using the Illumina Hiseq4000 or NovaSeq instruments, obtaining approximately 100-200 mln reads per 96 cells.
10X genomics:
For the 10x Genomics scRNA-Seq protocol up to 20,000 cells were pooled in pairs corresponding to male and female animals, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3' v3 protocol following the manufacturer's instructions.
Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cells.

treatment_protocol: Mice were treated with tamoxifen to induce a persistent fluorescent label, cells were harvested at indicated time intervals

tag: tissue

value: bone marrow

tag: cell type

value: Lin-negative, (cKit OR Sca1)-positive

tag: genotype

value: WT

tag: treatment


title: 3d7d_SS2_146814.46d [SLX-19981.i727_i513]


title: WT-Bone Marrow , H3R2me2a, EPIGENTEK,rep1

city: Wuhan

first: Haojian

last: Zhang

address: Donghu Rd.

country: China

institute: Wuhan University

library_source: genomic

molecule: genomic DNA

growth_protocol: IMDM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin,10μg/ml m-IL3,10μg/ml m-IL6,20μg/ml m-SCF.Cells were cultured at 37C at 5% CO2.

tag: cell line

value: Bone Marrow

tag: chip antibody


title: WT-Bone Marrow , H3R2me2a, EPIGENTEK,rep2


title: 3d7d_SS2_146814.46d [SLX-19981.i729_i513]


title: Prmt6KO-Bone Marrow , input


title: 3d7d_SS2_146814.46d [SLX-19981.i728_i513]


title: 3d7d_SS2_146814.46d [SLX-19981.i724_i513]


title: 3d7d_SS2_146814.46d [SLX-19981.i721_i515]


title: ChIP-seq of H3K4me1 in WT

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

data_processing:
For quantification of repetitive genomic regions, we allowed multiple-mapping reads using Bowtie2 parameter ‘–fast -k 1’.
Peak calling was performed with the MACS2 and TE-specific peaks were selected by overlapping with the RepeatMasker from UCSC (mm9.rmsk) using bedtools
Assembly: mm9
Supplementary files format and content: bigWig

source_name: mES

extract_protocol:
For ChIP-seq,cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of beads and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq Universal SYBR Green Supermix (Bio-Rad) on CFX96 (Bio-Rad).
ChIP-seq libraries were prepared with Illumina's ChIP-seq sample prep kit (0801-0303). NEBNext® DNA Library Prep Master Mix Set for Illumina.

value: mES

value: mouse embryonic stem cell


title: Prmt6KO-Bone Marrow , H3R2me2a, EPIGENTEK,rep2


title: 3d7d_SS2_146814.46d [SLX-19981.i720_i513]


title: Igf2bp2KO-Bone Marrow , input


title: 3d7d_SS2_146814.46d [SLX-19981.i722_i513]


title: Prmt6KO-Bone Marrow , H3R2me2a, EPIGENTEK,rep1


title: 3d7d_SS2_146814.46d [SLX-19981.i721_i513]


title: Igf2bp2KO-Bone Marrow , H3R2me2a, EPIGENTEK,rep1


title: 3d7d_SS2_146814.46d [SLX-19981.i719_i513]


title: Igf2bp2KO-Bone Marrow , H3R2me2a, EPIGENTEK,rep2


title: HiC_Th1_Ets1-SE-KO_Rep1B_Rep1T

city: Philadelphia

first: Golnaz

last: Vahedi

state: PA

address: 421 Curie Blvd

department: Department of Genetics

country: USA

institute: University of Pennsylvania

data_processing:
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.8.1) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GAATAATC,GAATACTC,GAATAGTC,GAATATTC,GAATGATC,GACTAATC,GACTACTC,GACTAGTC,GACTATTC,GACTGATC,GAGTAATC,GAGTACTC,GAGTAGTC,GAGTATTC,GAGTGATC,GATCAATC,GATCACTC,GATCAGTC,GATCATTC,GATCGATC,GATTAATC,GATTACTC,GATTAGTC,GATTATTC,GATTGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The valid pairs (allValidPairs file) from HiC-Pro were used to generate .hic file using Juicer tools (version 1.7.6) ‘pre’ command.
Valid pairs (VI), self-circle (SC) and dangling-end (DE) interactions in cis were used as input for significant interaction calling in ‘.bedpe’ format. Mango (version 1.2.0) step 4 identified putative significant interaction anchors by MACS peak calling (Zhang et al., 2008) with MACS_qvalue = 0.05 and MACS_shiftsize = 75. Mango step 5 identified significant interactions with default parameters except maxinteractingdist = 2000000 and MHT = found. In NOD mice, the BEDPE was shifted to BL6 coordinates with MMARGE (PMID: 29893919) utilizing the NOD VCF files (version 5) from the Mouse Genomes Project (PMID: 21921910).
Assembly: GRCm38
Supplementary files format and content: hic file obtained from Juicer tools.

source_name: Th1 cells

extract_protocol:
Hi-C libraries were generated on 1×106 cells using with Arima-HiC+ kit (Arima Genomics) following manufacturer's recommendations.
Library was prepared using Accel-NGS @S Plus DNA Library kit (21024 Swift Biosciences), according to the manufacturer’s recommendations. Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (66bp+66bp) on NovaSeq 6000 (Illumina).

treatment_protocol: Spleen of mice were dissociated through a 70µM mesh filter (Falcon) in RPMI 1640 (Corning), red blood cells were depleted using ACK lysis buffer (Gibco, Invitrogen). Naive CD4+ T cells were selected using negative selection beads (StemCell, Cat# 19765). For in vitro polarization, flat bottom 96-well plates were coated with 2 mg/mL of anti-CD3 (Clone: 145-2C11, BioLegend, Cat#100302) in PBS overnight at 4°C or 4 hrs at 37°C. For Th1 polarization, naive CD4+ T cells were cultured in RPMI 1640 medium (Invitrogen), supplemented with 10% fetal bovine serum (Fisher Scientific), 1mM sodium pyruvate (Gibco), 1% non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 1% HEPES (Gibco), 1% penicillin-streptomycin and 0.1% 2-Mercaptoethanol (Gibco).  For Th1 polarization, 0.2x106 naive CD4+ T cells were cultured in presence of 10 ng/mL of recombinant IL-12 (BioLegend, Cat#577002), 1 ng/mL of recombinant IL-2 (BioLegend, Cat#575402) and 1 mg/mL of soluble anti-CD28 (Clone: 37.51, BD Biosciences, Cat# 553294) for 6 days at 37°C.

value: Thymus

tag: strain


title: HiC_Th1_WT_Rep1B_Rep1T


title: hMeDIP-seq in Ell3 KO

data_processing:
For quantification of repetitive genomic regions, allowed multiple-mapping reads using Bowtie2 parameter ‘–fast -k 1’.
Assembly: mm9

growth_protocol: Feeder-free Mouse V6.5 embryonic stem cells were cultured on 0.1% gelatin-coated plates. mESCs were cultured in N2B27 medium (50% DMEM/F12 and 50%Neurobasal medium, 1x N2 supplement, 1x B27 supplement ,1x Penicillin-Streptomycin, 0.1 mM mercaptoethanol, 2 mM L-glutamine) supplemented with Mek inhibitor (PD0325901, 2.5 M),Gsk3 inhibitor (CHIR99021, 7.5 M) and 5 units of LIF, at 37°C with 5% CO2 in a humidified incubator and routinely passaged 2-3 times a week.

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature.5 μg of genomic DNA was sheared into 200-500 bp using Bioruptor (Diagenode) for 13 cycles with 30s on, 60s off. Sonicated DNA was immunoprecipitated with 5 μg of 5hmc antibody for 2 hrs at 4  °C, then Protein A/G beads was added into the DNA-antibody mixture and samples were incubated for another 2 hrs at 4  °C. DNA was purified from the elutant using FastPure Gel DNA Extraction Mini Kit (Vazyme).
The sequencing library was generated from purified ssDNA (10 ng) with Scale ssDNA-seq Lib Prep Kit (Abclonal) and amplified by PCR. Libraries with different indexes were pooled and sequenced using Illumina HiSeq sequencing systems.
hMeDIP-seq

value: mouse embryonic stem cells

value: ELL3 sgRNA

value: Active motif 39769


title: 3d7d_SS2_146814.46d [SLX-19981.i716_i513]


title: hMeDIP-seq in WT

value: non


title: 3d7d_SS2_146814.46f [SLX-19981.i728_i511]


title: 3d7d_SS2_146814.46f [SLX-19981.i729_i511]


title: m3.IRF8.KO.PC

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description:
m3.IRF8.KO.PC.rpkm
IRF8_actB.PC.geneRpkm.detected.csv

library_source: transcriptomic

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: csv file of RPKM normalized read counts for each detected gene

molecule: polyA RNA

source_name: spleen

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: Activated B cells and plasmablasts were derived from cultures of naïve B cells that were stimulated for 72 hours with 20 mg/ml LPS, 5 ng/ml IL-5, and 20 ng/ml IL-2

value: spleen

value: Plasma cell

tag: sorting markers

value: IRF8 KO

tag: irf8 sgrna

value: sgRNA 1

value: LPS, IL2, IL5 for 72 hrs


title: m3.IRF8.WT.B_cell

description:
m3.IRF8.WT.B_cell.rpkm
IRF8_actB.PC.geneRpkm.detected.csv

value: activated B cell

value: IRF8 WT


title: 3d7d_SS2_146814.46d [SLX-19981.i723_i513]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive


title: m3.IRF8.KO.B_cell

description:
m3.IRF8.KO.B_cell.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: m2.IRF8.WT.PC

description:
m2.IRF8.WT.PC.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: 3d7d_SS2_146814.46f [SLX-19981.i726_i511]

value: WT


title: 3d7d_SS2_146814.46f [SLX-19981.i724_i511]


title: 3d7d_SS2_146814.46f [SLX-19981.i723_i511]


title: 3d7d_SS2_146814.46f [SLX-19981.i727_i511]


title: 3d7d_SS2_146814.46f [SLX-19981.i719_i511]


title: 3d7d_SS2_146814.46f [SLX-19981.i721_i511]


title: 3d7d_SS2_146814.46f [SLX-19981.i720_i511]


title: m2.IRF8.KO.B_cell

description:
m2.IRF8.KO.B_cell.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: m2.IRF8.KO.PC

description:
m2.IRF8.KO.PC.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: 3d7d_SS2_146814.46f [SLX-19981.i722_i511]


title: 3d7d_SS2_146814.46d [SLX-19981.i718_i513]


title: m1.IRF8.KO.PC

description:
m1.IRF8.KO.PC.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: m1.IRF8.KO.B_cell

description:
m1.IRF8.KO.B_cell.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: 3d7d_SS2_146814.46f [SLX-19981.i716_i511]


title: 3d7d_SS2_146814.46f [SLX-19981.i729_i510]


title: 3d7d_SS2_146814.46f [SLX-19981.i728_i510]


title: RNa-seq of Ell3 KO-FA rep 2

data_processing:
RNA-seq reads were aligned to the Mus musculus genome (UCSC genome mm9) by HISAT2(v2.1.0) with default parameters. Read counts were calculated by HTSeq (v0.6.1.post1) using mapped reads, and differentially expressed genes were identified by DESeq2 (v1.36.0) (adjusted P-value<0.05, fold-change >0.58 either up- or down-regulation).
Assembly: mm9

growth_protocol: Feeder-free Mouse V6.5 embryonic stem cells were cultured on 0.1% gelatin-coated plates. mESCs were cultured in N2B27 medium (50% DMEM/F12 and 50%Neurobasal medium, 1× N2 supplement, 1× B27 supplement ,1× Penicillin-Streptomycin, 0.1 mM mercaptoethanol, 2 mM L-glutamine) supplemented with Mek inhibitor (PD0325901, 2.5 M),Gsk3 inhibitor (CHIR99021, 7.5 M) and 5 units of LIF. EpiSC cells were cultured on fibronectin-coated plates (5 g/mL/cm2) in N2B27 medium supplemented with Fgf2 (12 ng/mL) and Activin A (20 ng/mL) at 37°C with 5% CO2 in a humidified incubator and routinely passaged 2-3 times a week.

extract_protocol: RNAs from two independent biological replicates of ESCs and EpiSCs were extracted with QIAGEN RNeasy Mini Kit. Harvest around of 1 x 106 cells, as a cell pellet or by direct lysis in the vessel.Add 350μl of Buffer RLT. Add 1 volume of 70% ethanol to the lysate and mix well by pipetting. Transfer the sample to a spincolumn placed in a 2 ml collection tube and centrifuge for 1min at 10000 x g. Discard the flow-through. Add 700 μl Buffer RW1 to the RNeasy spin column. Close the lid and centrifuge for 15 s at ≥8000 x g. Discard the flow-through. Add 500 μl Buffer RPE to the spin column. Centrifuge for 1min at 10000x g and discard the flow-through. Then wash samples with 500 μl Buffer RPE in the spin column and elute the RNA with 30–50 μl RNase-free water.


title: RNA-seq of Ell3 KO-FA rep 1


title: RNA-seq of WT-FA rep 2


title: 3d7d_SS2_146814.46f [SLX-19981.i727_i510]


title: m2.IRF8.WT.B_cell

description:
m2.IRF8.WT.B_cell.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: 3d7d_SS2_146814.46f [SLX-19981.i726_i510]


title: m1.IRF8.WT.PC

description:
m1.IRF8.WT.PC.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: RNA-seq of WT-FA rep 1


title: 3d7d_SS2_146814.46f [SLX-19981.i724_i510]


title: RNA-seq of Ell3 KO-2iL rep 2


title: m1.IRF8.WT.B_cell

description:
m1.IRF8.WT.B_cell.rpkm
IRF8_actB.PC.geneRpkm.detected.csv


title: 3d7d_SS2_146814.46f [SLX-19981.i722_i510]


title: 3d7d_SS2_146814.46f [SLX-19981.i718_i511]


title: 3d7d_SS2_146814.46f [SLX-19981.i723_i510]


title: 3d7d_SS2_146814.46f [SLX-19981.i720_i510]


title: RNA-seq of WT-2iL rep 2


title: ChIP-seq of H3K27ac in Ell3 KO

data_processing:
For quantification of repetitive genomic regions, we allowed multiple-mapping reads using Bowtie2 parameter ‘–fast -k 1’.
Peak calling was performed with the MACS2 and TE-specific peaks were selected by overlapping with the RepeatMasker from UCSC (mm9.rmsk) using bedtools
Assembly: mm9

extract_protocol:
For ChIP-seq,cells were crosslinked with 1% formaldehyde for 10 min and quenched with glycine for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of beads and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq™ Universal SYBR® Green Supermix (Bio-Rad) on CFX96 (Bio-Rad).
ChIP-seq libraries were prepared with Illumina's ChIP-seq sample prep kit (0801-0303). NEBNext® DNA Library Prep Master Mix Set for Illumina.

value: Abclonal A7253


title: 3d7d_SS2_146814.46f [SLX-19981.i716_i510]


title: ChIP-seq of H3K27ac in WT


title: 3d7d_SS2_146814.46f [SLX-19981.i721_i510]


title: 3d7d_SS2_146814.46f [SLX-19981.i718_i510]


title: RNA-seq of WT-2iL rep 1


title: RNA-seq of Ell3 KO-2iL rep1


title: 3d7d_SS2_146814.46f [SLX-19981.i729_i508]


title: 3d7d_SS2_146814.46f [SLX-19981.i719_i510]


title: 3d7d_SS2_146814.46f [SLX-19981.i728_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i728_i520]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20566_scB5Tom_3dr2_ss2_fcounts.txt


title: ChIP-seq of Input


title: 3dr2_SS2_1468.23.97b [SLX-20556.i727_i520]


title: 3d7d_SS2_146814.46f [SLX-19981.i727_i508]


title: 3d7d_SS2_146814.46f [SLX-19981.i726_i508]


title: 3d7d_SS2_146814.46f [SLX-19981.i724_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i724_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i726_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i723_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i722_i520]


title: 3d7d_SS2_146814.46f [SLX-19981.i722_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i721_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i720_i520]


title: 3d7d_SS2_146814.46f [SLX-19981.i723_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i729_i520]


title: 3d7d_SS2_146814.46f [SLX-19981.i721_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i719_i520]


title: 3d7d_SS2_146814.46f [SLX-19981.i719_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i718_i520]


title: 3d7d_SS2_146814.46f [SLX-19981.i718_i508]


title: 3d7d_SS2_146814.46f [SLX-19981.i720_i508]


title: 3d7d_SS2_146814.46f [SLX-19981.i716_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i729_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i716_i520]


title: 3d7d_SS2_146814.46f [SLX-19981.i728_i507]


title: 3d7d_SS2_146814.46f [SLX-19981.i727_i507]


title: 3d7d_SS2_146814.46f [SLX-19981.i729_i507]


title: 3d7d_SS2_146814.46f [SLX-19981.i723_i507]


title: 3d7d_SS2_146814.46f [SLX-19981.i724_i507]


title: 3d7d_SS2_146814.46f [SLX-19981.i726_i507]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i726_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i723_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i724_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i728_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i727_i518]


title: 3d7d_SS2_146814.46f [SLX-19981.i721_i507]


title: 3d7d_SS2_146814.46f [SLX-19981.i722_i507]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i722_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i721_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i720_i518]


title: 3d7d_SS2_146814.46f [SLX-19981.i719_i507]


title: 3d7d_SS2_146814.46f [SLX-19981.i720_i507]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i718_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i719_i518]


title: 3d7d_SS2_146814.46f [SLX-19981.i718_i507]


title: 3d7d_SS2_146814.46f [SLX-19981.i729_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i716_i518]


title: 3d7d_SS2_146814.46f [SLX-19981.i716_i507]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i729_i517]


title: 3d7d_SS2_146814.46f [SLX-19981.i728_i506]


title: 3d7d_SS2_146814.46f [SLX-19981.i724_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i728_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i727_i517]


title: 3d7d_SS2_146814.46f [SLX-19981.i726_i506]


title: 3d7d_SS2_146814.46f [SLX-19981.i727_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i726_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i724_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i723_i517]


title: 3d7d_SS2_146814.46f [SLX-19981.i723_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i720_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i721_i517]


title: 3d7d_SS2_146814.46f [SLX-19981.i720_i506]


title: 3d7d_SS2_146814.46f [SLX-19981.i721_i506]


title: 3d7d_SS2_146814.46f [SLX-19981.i719_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i718_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i716_i517]


title: 3d7d_SS2_146814.46f [SLX-19981.i716_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i728_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i720_i505]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i729_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i721_i505]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i727_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i719_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i718_i505]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i724_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i716_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i728_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i729_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i722_i517]


title: 3d7d_SS2_146811.44g [SLX-19981.i726_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i723_i516]


title: 3d7d_SS2_146814.46f [SLX-19981.i722_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i720_i516]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i721_i516]


title: 3d7d_SS2_146814.46f [SLX-19981.i718_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i719_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i722_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i724_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i718_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i722_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i723_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i719_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i721_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i716_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i720_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i719_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i729_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i726_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i716_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i718_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i728_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i727_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i727_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i726_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i724_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i723_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i722_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i729_i502]


title: 3d7d_SS2_146811.44g [SLX-19981.i728_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i720_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i726_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i718_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i721_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i719_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i723_i502]


title: 3d7d_SS2_146811.44g [SLX-19981.i722_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i729_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i728_i513]


title: 3d7d_SS2_146811.44g [SLX-19981.i719_i502]


title: 3d7d_SS2_146811.44g [SLX-19981.i720_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i727_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i726_i513]


title: 3d7d_SS2_146811.44g [SLX-19981.i716_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i724_i513]


title: 3d7d_SS2_146811.44g [SLX-19981.i714_i511]


title: 3d7d_SS2_146811.44g [SLX-19981.i727_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i721_i513]


title: 3d7d_SS2_146811.44g [SLX-19981.i715_i511]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i723_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i722_i513]


title: 3d7d_SS2_146811.44g [SLX-19981.i710_i511]


title: 3d7d_SS2_146811.44g [SLX-19981.i712_i511]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i720_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i716_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i711_i511]


title: 3d7d_SS2_146811.44g [SLX-19981.i707_i511]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i716_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i719_i513]


title: 3d7d_SS2_146811.44g [SLX-19981.i721_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i715_i522]


title: 3d7d_SS2_146811.44g [SLX-19981.i704_i511]


title: 3d7d_SS2_146811.44g [SLX-19981.i705_i511]


title: 3d7d_SS2_146811.44g [SLX-19981.i718_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i714_i522]


title: 3d7d_SS2_146811.44g [SLX-19981.i703_i511]


title: 3d7d_SS2_146811.44g [SLX-19981.i702_i511]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i711_i522]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i710_i522]


title: 3d7d_SS2_146811.44g [SLX-19981.i701_i511]


title: 3d7d_SS2_146811.44g [SLX-19981.i715_i510]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i707_i522]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i706_i522]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i705_i522]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i704_i522]


title: 3d7d_SS2_146811.44g [SLX-19981.i706_i511]


title: 3d7d_SS2_146811.44g [SLX-19981.i711_i510]


title: 3d7d_SS2_146811.44g [SLX-19981.i712_i510]


title: 3d7d_SS2_146811.44g [SLX-19981.i710_i510]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i715_i521]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i712_i522]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i701_i522]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i702_i522]


title: 3d7d_SS2_146811.44g [SLX-19981.i706_i510]


title: 3d7d_SS2_146811.44g [SLX-19981.i707_i510]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i714_i521]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i718_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i712_i521]


title: 3d7d_SS2_146811.44g [SLX-19981.i703_i510]


title: 3d7d_SS2_146811.44g [SLX-19981.i705_i510]


title: 3d7d_SS2_146811.44g [SLX-19981.i702_i510]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i711_i521]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i710_i521]


title: 3d7d_SS2_146811.44g [SLX-19981.i714_i510]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i703_i522]


title: 3d7d_SS2_146811.44g [SLX-19981.i704_i510]


title: 3d7d_SS2_146811.44g [SLX-19981.i701_i510]


title: 3d7d_SS2_146811.44g [SLX-19981.i715_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i707_i521]


title: 3d7d_SS2_146811.44g [SLX-19981.i711_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i712_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i714_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i710_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i724_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i705_i521]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i704_i521]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i706_i521]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i715_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i702_i521]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i703_i521]


title: 3d7d_SS2_146811.44g [SLX-19981.i704_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i705_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i714_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i712_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i711_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i701_i521]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i710_i520]


title: 3d7d_SS2_146811.44g [SLX-19981.i702_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i715_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i714_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i712_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i707_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i706_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i710_i507]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i702_i520]


title: 3d7d_SS2_146811.44g [SLX-19981.i703_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i711_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i707_i507]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i703_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i706_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i704_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i701_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i715_i518]


title: 3d7d_SS2_146811.44g [SLX-19981.i701_i508]


title: 3d7d_SS2_146811.44g [SLX-19981.i704_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i706_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i703_i507]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i707_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i712_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i711_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i714_i518]


title: 3d7d_SS2_146811.44g [SLX-19981.i702_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i701_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i705_i507]


title: 3d7d_SS2_146811.44g [SLX-19981.i715_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i707_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i710_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i705_i520]


title: 3d7d_SS2_146811.44g [SLX-19981.i714_i506]


title: 3d7d_SS2_146811.44g [SLX-19981.i712_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i705_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i704_i518]


title: 3d7d_SS2_146811.44g [SLX-19981.i711_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i703_i518]


title: 3d7d_SS2_146811.44g [SLX-19981.i710_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i702_i518]


title: 3d7d_SS2_146811.44g [SLX-19981.i707_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i701_i518]


title: 3d7d_SS2_146811.44g [SLX-19981.i706_i506]


title: 3d7d_SS2_146811.44g [SLX-19981.i704_i506]


title: 3d7d_SS2_146811.44g [SLX-19981.i705_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i715_i517]


title: 3d7d_SS2_146811.44g [SLX-19981.i703_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i711_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i710_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i712_i517]


title: 3d7d_SS2_146811.44g [SLX-19981.i702_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i706_i517]


title: 3d7d_SS2_146811.44g [SLX-19981.i715_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i714_i505]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i703_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i705_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i704_i517]


title: 3d7d_SS2_146811.44g [SLX-19981.i711_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i712_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i710_i505]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i702_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i701_i517]


title: 3d7d_SS2_146811.44g [SLX-19981.i707_i505]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i714_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i714_i516]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i715_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i706_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i705_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i701_i506]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i707_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i712_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i703_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i702_i505]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i710_i516]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i711_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i701_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i715_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i706_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i714_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i712_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i703_i516]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i705_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i710_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i711_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i707_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i704_i505]


title: 3d7d_SS2_146811.44g [SLX-19981.i706_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i704_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i705_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i703_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i714_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i715_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i707_i516]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i710_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i702_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i701_i503]


title: 3d7d_SS2_146811.44g [SLX-19981.i715_i502]


title: 3d7d_SS2_146811.44g [SLX-19981.i702_i503]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i704_i516]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i711_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i714_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i706_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i701_i516]


title: 3d7d_SS2_146811.44g [SLX-19981.i712_i502]


title: 3d7d_SS2_146811.44g [SLX-19981.i711_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i703_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i704_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i710_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i705_i515]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i702_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i706_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i712_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i707_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i701_i515]


title: 3d7d_SS2_146811.44g [SLX-19981.i704_i502]


title: 3d7d_SS2_146811.44g [SLX-19981.i705_i502]


title: 3d7d_SS2_146811.44g [SLX-19981.i703_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i715_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i714_i513]


title: 3d7d_SS2_146811.44g [SLX-19981.i702_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i712_i513]


title: 3d7d_SS2_146811.44g [SLX-19981.i701_i502]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i711_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i707_i515]


title: 7d_SS2_14681.30e [SLX-19435.i729_i521]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX19435_scB5Tom_7d_ss2_fcounts.txt


title: 3dr2_SS2_1468.23.97b [SLX-20556.i707_i513]


title: 7d_SS2_14681.30e [SLX-19435.i729_i520]


title: 7d_SS2_14681.30e [SLX-19435.i729_i522]


title: 7d_SS2_14681.30e [SLX-19435.i729_i518]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i705_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i704_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i706_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i703_i513]


title: 7d_SS2_14681.30e [SLX-19435.i729_i515]


title: 7d_SS2_14681.30e [SLX-19435.i729_i516]


title: 7d_SS2_14681.30e [SLX-19435.i729_i517]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i702_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i706_i511]


title: 7d_SS2_14681.30e [SLX-19435.i729_i513]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i701_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i705_i511]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i704_i511]


title: 7d_SS2_14681.32c [SLX-19435.i728_i522]


title: 7d_SS2_14681.30e [SLX-19435.i728_i520]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i710_i513]


title: 7d_SS2_14681.32c [SLX-19435.i728_i521]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i703_i511]


title: 7d_SS2_14681.30e [SLX-19435.i728_i518]


title: 7d_SS2_14681.30e [SLX-19435.i728_i517]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i701_i511]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i702_i511]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i715_i510]


title: 7d_SS2_14681.30e [SLX-19435.i728_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i714_i510]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i711_i510]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i712_i510]


title: 7d_SS2_14681.30e [SLX-19435.i727_i521]


title: 7d_SS2_14681.30e [SLX-19435.i728_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i710_i510]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i707_i510]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i705_i510]


title: 7d_SS2_14681.30e [SLX-19435.i727_i518]


title: 7d_SS2_14681.30e [SLX-19435.i727_i520]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i706_i510]


title: 7d_SS2_14681.30e [SLX-19435.i727_i517]


title: 7d_SS2_14681.30e [SLX-19435.i727_i516]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i704_i510]


title: 7d_SS2_14681.32c [SLX-19435.i726_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i703_i510]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i715_i508]


title: 7d_SS2_14681.30e [SLX-19435.i727_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i702_i510]


title: 7d_SS2_14681.30e [SLX-19435.i727_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i701_i510]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i714_i508]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i712_i508]


title: 7d_SS2_14681.30e [SLX-19435.i726_i518]


title: 7d_SS2_14681.32c [SLX-19435.i726_i521]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i711_i508]


title: 7d_SS2_14681.30e [SLX-19435.i726_i517]


title: 7d_SS2_14681.30e [SLX-19435.i726_i516]


title: 7d_SS2_14681.30e [SLX-19435.i726_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i710_i508]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i707_i508]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i706_i508]


title: 7d_SS2_14681.30e [SLX-19435.i724_i522]


title: 7d_SS2_14681.30e [SLX-19435.i724_i521]


title: 7d_SS2_14681.30e [SLX-19435.i726_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i705_i508]


title: 3dr2_SS2_1468.23.97b [SLX-20556.i706_i518]


title: 7d_SS2_14681.30e [SLX-19435.i724_i520]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i704_i508]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i703_i508]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i702_i508]


title: 7d_SS2_14681.30e [SLX-19435.i724_i517]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i701_i508]


title: 7d_SS2_14681.30e [SLX-19435.i724_i516]


title: 7d_SS2_14681.30e [SLX-19435.i724_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i714_i507]


title: 7d_SS2_14681.32c [SLX-19435.i723_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i712_i507]


title: 7d_SS2_14681.32c [SLX-19435.i723_i521]


title: 7d_SS2_14681.32c [SLX-19435.i723_i520]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i707_i507]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i706_i507]


title: 7d_SS2_14681.30e [SLX-19435.i723_i517]


title: 7d_SS2_14681.30e [SLX-19435.i723_i518]


title: 7d_SS2_14681.30e [SLX-19435.i724_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i705_i507]


title: 7d_SS2_14681.30e [SLX-19435.i723_i515]


title: 7d_SS2_14681.30e [SLX-19435.i724_i518]


title: 7d_SS2_14681.30e [SLX-19435.i723_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i703_i507]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i704_i507]


title: 7d_SS2_14681.30e [SLX-19435.i723_i516]


title: 7d_SS2_14681.30e [SLX-19435.i722_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i715_i507]


title: 7d_SS2_14681.30e [SLX-19435.i722_i520]


title: 7d_SS2_14681.30e [SLX-19435.i722_i521]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i715_i506]


title: 7d_SS2_14681.30e [SLX-19435.i722_i518]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i710_i507]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i701_i507]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i714_i506]


title: 7d_SS2_14681.30e [SLX-19435.i722_i517]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i711_i506]


title: 7d_SS2_14681.30e [SLX-19435.i722_i516]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i710_i506]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i712_i506]


title: 7d_SS2_14681.30e [SLX-19435.i722_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i707_i506]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i702_i507]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i711_i507]


title: 7d_SS2_14681.32c [SLX-19435.i721_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i706_i506]


title: 7d_SS2_14681.32c [SLX-19435.i721_i521]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i705_i506]


title: 7d_SS2_14681.32c [SLX-19435.i721_i520]


title: 7d_SS2_14681.30e [SLX-19435.i721_i517]


title: GB7047 (WT Tam 2)

city: Bethesda

first: Jinfang

last: Zhu

state: MD

address: 10 Center Drive, Building 10, Room 11D02

department: National Institute of Allergy and Infectious Disease

institute: National Institutes of Health

data_processing:
Multiplex sequencing reads of 50 bp were generated by the NHLBI DNA Sequencing and Computational Biology Core and sequence reads were mapped to the mouse genome (mm9) using bowtie 2 with the default settings. Gene expression was measured by RPKM and differentially expressed genes were identified using Partek Flow (Partek).
Assembly: mm9
Supplementary files format and content: GB7041toGB7048.rpkm.txt - a csv txt file containing the RPKM values for all 8 libraries.

source_name: Cd45.1/Cd45.2 CD3+CD4+CD44 high T effector cells, tamoxifen treated, mixed congenic transfer recipient host 2

extract_protocol:
Single cell suspension were prepared from the brain and spinal cords of mixed congenic receipient EAE mice via digestion with 1 U/ml Liberase TM (Roche) and 0.3 U/ml DNase I (Roche) in incomplete RPMI1640 media for 30 minutes at 37C. The tissues were mechanically disrupted via repetitive pipetting and filtered through a 70μm cell strainer (Fisher Scientific). The resulting cell suspension was centrifuged through a percoll density gradient (38% - 70%) and mononuclear cells were collected from the interphase. CNS-infiltrating CD4 T effector cells (i.e., CD45.1+CD45.2+ CD3+CD4+CD44 high wild type T cells or CD45.2+CD3+CD4+CD44 high Cre-ERT2 Gata3 Fl/Fl T cells) were isolated by FACS sorting.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed congenic transfer Tcra-/- recipient mice received MOG/IFA, Pertussis Toxin (day 0 and day 2), and corn oil or tamoxifen in corn oil on day 0 of the experiment as decribed in the methods.

value: Brain and spinal cord (CNS)

value: CD3+CD4+CD44 high effector T cells

value: Tamoxifen, day 0


title: 7d_SS2_14681.30e [SLX-19435.i722_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i704_i506]


title: GB7045 (WT Tam 1)

source_name: Cd45.1/Cd45.2 CD3+CD4+CD44 high T effector cells, tamoxifen treated, mixed congenic transfer recipient host 1


title: 7d_SS2_14681.30e [SLX-19435.i721_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i703_i506]


title: GB7044 (Gata3 cKO Veh 2)

source_name: Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl CD3+CD4+CD44 high T effector cells, vehicle control, mixed congenic transfer recipient host 2

value: Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl

value: Corn oil, day 0


title: 7d_SS2_14681.30e [SLX-19435.i721_i513]


title: 7d_SS2_14681.30e [SLX-19435.i720_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i702_i506]


title: 7d_SS2_14681.30e [SLX-19435.i720_i521]


title: GB7043 (WT Veh 2)

source_name: Cd45.1/Cd45.2 CD3+CD4+CD44 high T effector cells, vehicle control, mixed congenic transfer recipient host 2


title: 7d_SS2_14681.30e [SLX-19435.i720_i520]


title: GB7048 (Gata3 cKO Tam 2)

source_name: Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl CD3+CD4+CD44 high T effector cells, tamoxifen treated, mixed congenic transfer recipient host 2


title: GB7042 (Gata3 cKO Veh 1)

source_name: Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl CD3+CD4+CD44 high T effector cells, vehicle control, mixed congenic transfer recipient host 1


title: 3dr2_SS2_1468.21.100e [SLX-20556.i715_i505]


title: 7d_SS2_14681.30e [SLX-19435.i720_i518]


title: 7d_SS2_14681.30e [SLX-19435.i720_i517]


title: 7d_SS2_14681.30e [SLX-19435.i721_i518]


title: GB7046 (Gata3 cKO Tam 1)

source_name: Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl CD3+CD4+CD44 high T effector cells, tamoxifen treated, mixed congenic transfer recipient host 1


title: 7d_SS2_14681.30e [SLX-19435.i720_i516]


title: GB7041 (WT Veh 1)

source_name: Cd45.1/Cd45.2 CD3+CD4+CD44 high T effector cells, vehicle control, mixed congenic transfer recipient host 1


title: 7d_SS2_14681.30e [SLX-19435.i721_i516]


title: 7d_SS2_14681.30e [SLX-19435.i720_i513]


title: 7d_SS2_14681.30e [SLX-19435.i720_i515]


title: 7d_SS2_14681.32c [SLX-19435.i719_i522]


title: 7d_SS2_14681.32c [SLX-19435.i719_i521]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i712_i505]


title: 7d_SS2_14681.32c [SLX-19435.i719_i520]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i711_i505]


title: 7d_SS2_14681.30e [SLX-19435.i719_i518]


title: 7d_SS2_14681.30e [SLX-19435.i719_i517]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i701_i506]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i710_i505]


title: 7d_SS2_14681.30e [SLX-19435.i727_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i707_i505]


title: 7d_SS2_14681.30e [SLX-19435.i719_i516]


title: Fermentation 4

type: RNA

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

description: Gene expression in MR-1(pBBR-glk-galP) grown in the absence of electron acceptors

hyb_protocol: For each array, 19 µL of the purified Cy3-labeled cRNA (600 ng) was mixed with 5 µL of 10× Blocking Agent, 1 µL of 25× Fragmentation Buffer, and 25 µL of 2× GE Hybridization Buffer HI-RPM. The resultant mixtures were hybridized to the arrays at 65ºC for 17 h. After hybridization, each microarray slide was washed with Gene Expression wash buffer 1 at room temperature for 1 min, followed by Gene Expression wash buffer 2 at 37ºC for 1min.

scan_protocol: Slides were air dried for 1 min and scanned using an Agilent DNA Microarray Scanner at 5-µm resolution.

data_processing: Gene expression data (fluorescent intensities) were extracted from the scanned image using the Feature Extraction Software version 8.1 (Agilent Technologies) and normalized and statistically analyzed using the limma software package (version 3.36.2; https://www.bioconductor.org/packages/release/bioc/html/limma.html)

organism: Shewanella oneidensis

source_name: MR-1(pBBR-glk-galP) inculabed under a fermentative condition 4

label_protocol: Cyanine3 (Cy3)-labeled cRNA was synthesized from 50 ng of total RNA using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) and purified using a RNeasy Mini Kit (Qiagen). The labeled cRNA was quantified using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: MR-1(pBBR-glk-galP) was grown in GMM supplemented with fumarate (40 mM) as an electron acceptor, and cells were harvested at the logarithmic growth phase (OD600 0.2–0.3). These cells were incubated for 3 h in the presence (the fumarate-respiring condition) or absence (the fermentative condition) of fumarate.

extract_protocol: Total RNA was extracted using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The extracted RNA was purified using an RNeasy Mini kit and RNase-Free DNase set (Qiagen, Valencia, CA, USA). The quality of purified RNA was evaluated using an Agilent 2100 Bioanalyzer, RNA 6000 Pico reagents, and RNA Pico chips (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The cell suspension was centrifuged at 13,000 rpm for 1 min to precipitate the cells.


title: 7d_SS2_14681.30e [SLX-19435.i719_i515]


title: Fermentation 2

source_name: MR-1(pBBR-glk-galP) inculabed under a fermentative condition 2

value: grown in the absence of electron acceptors


title: Fermentation 3

source_name: MR-1(pBBR-glk-galP) inculabed under a fermentative condition 3


title: 7d_SS2_14681.30e [SLX-19435.i718_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i714_i505]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i706_i505]


title: 7d_SS2_14681.30e [SLX-19435.i719_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i705_i505]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i704_i505]


title: 7d_SS2_14681.30e [SLX-19435.i718_i517]


title: 7d_SS2_14681.30e [SLX-19435.i718_i521]


title: 7d_SS2_14681.30e [SLX-19435.i718_i518]


title: 7d_SS2_14681.30e [SLX-19435.i718_i520]


title: 7d_SS2_14681.30e [SLX-19435.i718_i516]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i702_i505]


title: 7d_SS2_14681.30e [SLX-19435.i718_i513]


title: 7d_SS2_14681.32c [SLX-19435.i716_i522]


title: Respiration 2

description: Gene expression in MR-1(pBBR-glk-galP) grown under a fumarate-respiring condition

source_name: MR-1(pBBR-glk-galP) inculabed under a fumarate-respiring condition 2


title: Respiration 1

source_name: MR-1(pBBR-glk-galP) inculabed under a fumarate-respiring condition 1

value: grown under a fumarate-respiring condition


title: Respiration 3

source_name: MR-1(pBBR-glk-galP) inculabed under a fumarate-respiring condition 3


title: Fermentation 1

source_name: MR-1(pBBR-glk-galP) inculabed under a fermentative condition 1


title: 3dr2_SS2_1468.21.100e [SLX-20556.i701_i505]

source_name: bone marrow


title: SS5-siG3BP2

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
Sequenced reads were trimmed for adaptor sequence using Fastp, and then mapped to hg38. p13. whole genome using HiSat2 version 2.1.0 with defalt parameters.
Transcripts Per Million (TPM) were calculated.
Assembly: hg38. p13.
Supplementary files format and content: TPMs of G3BP1 KD and SG.csv

organism: Homo sapiens

growth_protocol: SH-SY5Y cells were grown with 5% CO2 at 37°C in culture medium prepared from Advanced DMEM/F-12 supplemented with 10% FBS, 1×GlutaMAX I, and 1×Penicillin-Streptomycin.

extract_protocol:
For KD RNA-seq and SG RNA-seq, total RNAs were isolated using ISOGEN II following the manufacturer’s instructions. For eCLIP-seq, G3BP1- and G3BP2-bound RNAs were isolated using their antibodies as .
For KD and SG RNA-seq, RNA libraries were prepared for sequencing using standard DNBSEQ protocols. For eCLIP-seq, RNA libraries were prepared according to the eCLIP-seq protocol in König et al., 2010.
KD and SG RNA-seq were polyA RNA-Seq, whereas eCLIP-seq was manurally constructed according to the eCLIP-seq protocol in König et al., 2010.

treatment_protocol: SH-SY5Y cells were treated with 50 mM Sodium arsenite for 1 hr.


title: 7d_SS2_14681.30e [SLX-19435.i716_i518]


title: 7d_SS2_14681.30e [SLX-19435.i716_i517]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i715_i503]


title: SS5-Total


title: SS5-siCtrl


title: 3dr2_SS2_1468.21.100e [SLX-20556.i712_i503]


title: 7d_SS2_14681.30e [SLX-19435.i716_i513]


title: SS5-siG3BP1


title: 7d_SS2_14681.30e [SLX-19435.i716_i516]


title: 7d_SS2_14681.30e [SLX-19435.i715_i522]


title: Respiration 4

source_name: MR-1(pBBR-glk-galP) inculabed under a fumarate-respiring condition 4


title: SS5-SG


title: 3dr2_SS2_1468.21.100e [SLX-20556.i703_i505]


title: 7d_SS2_14681.30e [SLX-19435.i718_i515]


title: 7d_SS2_14681.30e [SLX-19435.i715_i521]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i714_i503]


title: 7d_SS2_14681.32c [SLX-19435.i716_i521]


title: 7d_SS2_14681.30e [SLX-19435.i715_i520]


title: 7d_SS2_14681.32c [SLX-19435.i716_i520]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i711_i503]


title: 7d_SS2_14681.30e [SLX-19435.i715_i518]


title: 7d_SS2_14681.30e [SLX-19435.i728_i516]


title: SS5-ctrl

description: rRNA-depleted RNA-seq of control SH-SY5Y cell

data_processing:
Sequenced reads were trimmed for adaptor sequence using Fastp, and then mapped to hg38. p13. whole genome using HiSat2 version 2.1.0 with defalt parameters.
Transcripts Per Million (TPM) were calculated.
Genome_build: hg38. p13.

extract_protocol:
Total RNAs were isolated using ISOGEN II following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

treatment_protocol: No treatment control

value: neuroblastoma

value: control


title: 7d_SS2_14681.30e [SLX-19435.i715_i517]


title: 7d_SS2_14681.30e [SLX-19435.i716_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i710_i503]


title: 7d_SS2_14681.30e [SLX-19435.i715_i516]


title: 7d_SS2_14681.30e [SLX-19435.i715_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i707_i503]


title: 7d_SS2_14681.30e [SLX-19435.i715_i513]


title: HFFF cells mock infected, PAA treated, histone H1, replicate 1

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: DNA isolated with Zymo DNA Clean & Concentrator

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph

source_name: ChIPmentation

growth_protocol: HFFFs were cultured in DMEM supplements with 10% FBS and P/S. Cells were infected with WT HSV-1 (strain 17 or F) or ICP22-null mutant at an MOI of 10. Marked samples were treated with 350 µg/ml PAA throught the course of infection

extract_protocol:
Samples were processed according to the ChIPmentation protocol with few adjustments indicated in Materials and Methods (Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015)
See Schmidl C et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Methods. 2015, Oct;12(10):963-965. doi: 10.1038/nmeth.3542. Epub 2015 Aug 17. PMID: 26280331; PMCID: PMC4589892.
Paired-end sequencing

treatment_protocol: Cells were infected with WT HSV-1 for 15 min or ΔICP22 for 1 hour using an MOI of 10. After infection, cell culture media was replaced with fresh media in which the PAA was added. Samples were crosslinked and collected at the indicated time points and afterwards processed according to the ChIPmentation protocol.

value: Human fetal foreskin fibroblasts

value: PAA (350 microg/ml)

tag: infection

value: mock


title: HFFF cells infected with ΔICP22 (F), 8hpi, PAA treated, histone H1, replicate 2

value: deltaICP22, strain F


title: 3dr2_SS2_1468.21.100e [SLX-20556.i705_i503]

value: bone marrow


title: 7d_SS2_14681.30e [SLX-19435.i714_i522]

value: Lin-negative, (cKit OR Sca1)-positive


title: 7d_SS2_14681.30e [SLX-19435.i714_i520]

value: WT


title: 7d_SS2_14681.30e [SLX-19435.i714_i516]


title: 7d_SS2_14681.30e [SLX-19435.i714_i521]


title: 7d_SS2_14681.30e [SLX-19435.i714_i518]


title: 7d_SS2_14681.30e [SLX-19435.i714_i517]


title: HFFF cells infected with HSV-1 WT (F), 8hpi, PAA treated, histone H1, replicate 2

value: HSV-1 WT, strain F


title: 7d_SS2_14681.30e [SLX-19435.i714_i515]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i704_i503]


title: HFFF cells infected with ΔICP22 (F), 8hpi, PAA treated, histone H1, replicate 1


title: HFFF cells infected with HSV-1 WT (F), 8hpi, PAA treated, histone H1, replicate 1


title: 3dr2_SS2_1468.21.100e [SLX-20556.i703_i503]


title: HFFF cells mock infected, PAA treated, histone H1, replicate 2


title: 7d_SS2_14681.30e [SLX-19435.i712_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i702_i503]


title: 7d_SS2_14681.30e [SLX-19435.i712_i520]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i701_i503]


title: 7d_SS2_14681.30e [SLX-19435.i712_i517]


title: HFFF cells mock 8h infected, PAA treated, histone H3K36me3, replicate 1


title: 3dr2_SS2_1468.21.100e [SLX-20556.i706_i503]


title: HFFF cells mock 8h infected, PAA treated, histone H3K36me3, replicate 2


title: 7d_SS2_14681.30e [SLX-19435.i712_i518]


title: 7d_SS2_14681.30e [SLX-19435.i712_i516]


title: HFFF cells mock 8h infected, PAA treated, histone H3K27me3, replicate 2


title: 3dr2_SS2_1468.21.100e [SLX-20556.i715_i502]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i714_i502]


title: 7d_SS2_14681.30e [SLX-19435.i712_i515]


title: 7d_SS2_14681.30e [SLX-19435.i714_i513]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i711_i502]


title: 7d_SS2_14681.30e [SLX-19435.i711_i518]


title: 7d_SS2_14681.30e [SLX-19435.i711_i521]


title: 7d_SS2_14681.30e [SLX-19435.i712_i513]


title: 7d_SS2_14681.30e [SLX-19435.i711_i522]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i712_i502]


title: 7d_SS2_14681.30e [SLX-19435.i712_i521]


title: HFFF cells mock 8h infected, PAA treated, histone H3K27me3, replicate 1


title: HFFF cells mock 8h infected, PAA treated, histone H4, replicate 2


title: 7d_SS2_14681.30e [SLX-19435.i711_i520]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i710_i502]


title: 7d_SS2_14681.30e [SLX-19435.i711_i517]


title: HFFF cells mock 8h infected, PAA treated, histone H4, replicate 1


title: HFFF cells mock 8h infected, PAA treated, histone H3, replicate 1


title: 7d_SS2_14681.30e [SLX-19435.i711_i515]


title: HFFF cells mock 8h infected, PAA treated, histone H1, replicate 2


title: 45M

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

scan_protocol: Gene expression analysis was conducted using the NanoString nCounter platform (NanoString Technologies)

data_processing: Based on an extensive literature review, we selected a custom code set consisting of a panel of 41 genes involved in DNA repair and immune response pathways, molecular subtyping, or other relevant cellular processes. ACTB, GAPDH, HPRT1, and LDHA were used as endogenous controls. The raw NanoString data was normalized according to the manufacturer’s instructions, followed by a log-transformation to ensure normal distribution. Samples and genes with >75% of expression values lower than the negative control were filtered out. Gene expression heatmaps were generated to visualize possible patterns of expression.

source_name: Muscle-invasive bladder cancer patients treated with neoadjuvant chemotherapy

extract_protocol: H&E-stained sections of TURBT formalin-fixed paraffin-embedded (FFPE) samples were reviewed to identify areas enriched in tumor cells (>30%); consecutive 10-μm sections were used to macrodissect the selected areas and isolate RNA. Samples were sheared by sonication with a S2 Covaris instrument (Wobrun, MA). RNA was purified using the truXTRAC FFPE microTube RNA Kit (Covaris) following the manufacturer’s instructions, eluted in a final volume of 30 µl, and immediately quantified using the Qubit 3 Fluorometer (Thermo Fisher Scientific

tag: disease

value: Muscle-invasive bladder cancer

tag: agent

value: neoadjuvant chemotherapy


title: 46M


title: 43M


title: 47M


title: 3dr2_SS2_1468.21.100e [SLX-20556.i703_i502]


title: HFFF cells mock 8h infected, PAA treated, histone H3, replicate 2


title: HFFF cells mock 8h infected, PAA treated, histone H1, replicate 1


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3K36me3, replicate 1

value: HSV-1 WT, strain 17


title: 3dr2_SS2_1468.21.100e [SLX-20556.i707_i502]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i702_i502]


title: 7d_SS2_14681.30e [SLX-19435.i711_i516]


title: 7d_SS2_14681.30e [SLX-19435.i710_i520]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i701_i502]


title: 7d_SS2_14681.30e [SLX-19435.i710_i521]


title: 39M


title: 3dr2_SS2_1468.21.100e [SLX-20556.i706_i502]


title: 3dr2_SS2_1468.21.100e [SLX-20556.i704_i502]


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3K27me3, replicate 2


title: 41M


title: 7d_SS2_14681.30e [SLX-19435.i710_i518]


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3K36me3, replicate 2


title: 42M


title: 38M


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3K27me3, replicate 1


title: 3dr2_SS2_1468.21.100e [SLX-20556.i705_i502]


title: 7d_SS2_14681.30e [SLX-19435.i711_i513]


title: 2w4w_SS2_146818.66b [SLX-20544.i729_i522]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20544_scB5Tom_2w_ss2_fcounts.txt


title: 7d_SS2_14681.30e [SLX-19435.i710_i522]


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H4, replicate 2


title: 7d_SS2_14681.30e [SLX-19435.i710_i517]


title: 2w4w_SS2_146818.66b [SLX-20544.i728_i522]


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H4, replicate 1


title: 35M


title: 32M


title: 7d_SS2_14681.30e [SLX-19435.i710_i516]


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3, replicate 1


title: 7d_SS2_14681.30e [SLX-19435.i710_i513]


title: 2w4w_SS2_146818.66b [SLX-20544.i727_i522]


title: 7d_SS2_14681.30e [SLX-19435.i710_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i726_i522]


title: 31M


title: 7d_SS2_14681.30e [SLX-19435.i707_i522]


title: 2w4w_SS2_146818.66b [SLX-20544.i724_i522]


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H1, replicate 2


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H1, replicate 1


title: 7d_SS2_14681.30e [SLX-19435.i707_i521]


title: 2w4w_SS2_146818.66b [SLX-20544.i723_i522]


title: 2w4w_SS2_146818.66b [SLX-20544.i722_i522]


title: 7d_SS2_14681.30e [SLX-19435.i707_i520]


title: 7d_SS2_14681.30e [SLX-19435.i707_i518]


title: 28M


title: 29M


title: 33M


title: 26M


title: 27M


title: 2w4w_SS2_146818.66b [SLX-20544.i721_i522]


title: 2w4w_SS2_146818.66b [SLX-20544.i720_i522]


title: 7d_SS2_14681.30e [SLX-19435.i707_i516]


title: 2w4w_SS2_146818.66b [SLX-20544.i719_i522]


title: 24M


title: 25M


title: 2w4w_SS2_146818.66b [SLX-20544.i718_i522]


title: 7d_SS2_14681.30e [SLX-19435.i707_i515]


title: 7d_SS2_14681.30e [SLX-19435.i707_i513]


title: 23M


title: 7d_SS2_14681.30e [SLX-19435.i706_i522]


title: 20M


title: NL97

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

description: SAMPLE 64

hyb_protocol: Labeled RNA was hybridized on microarray for 20hours at 55℃ by using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to the manufacturer’s protocol (protocol for use with Agilent microRNA microarrays Version 1.0).

scan_protocol: Hybridization signals were detected with a DNA microarray scanner G2505B (Agilent Technologies) and the scanned images were analyzed using Agilent feature extraction software (v9.5.3.1).

data_processing:
Data were analyzed using the GeneSpring GX10.0.2 (Agilent). Quality control (QC) was applied according to the manufacturer’s instructions, and all data were approved by GeneSpring.
We used raw data (gProcessedSignal) and normalized each expression so as to have zero mean and unit sample variance.

source_name: patient with normal liver

label_protocol: To detect serum miRNA, 60 ng of RNA was labeled using the Human microRNA Microarray Kit (Rel 14.0) (Agilent Technologies, CA, USA) according to the manufacturer’s protocol (protocol for use with Agilent microRNA microarrays Version 1.0).

growth_protocol: none listed

extract_protocol: Total RNA from 200 ul of serum was prepared using miRNeasy mini kit (Qiagen, Hilden Germany) according to the manufacturer’s instruction. Exosome rich fractionated RNA was prepared using Exoquick (System Biosciences, CA, USA). Briefly, 900 ul of serum was mixed with 250 ul of Exoquick and incubated for 12 hr at 4℃. The tubes were centrifuged at 1500 g for 30 min at room temperature and then supernatant was discarded. The pellet was dissolved with 200 ul of PBS with vigorous vortex. RNA was extracted using miRNeasy mini kit (Qiagen).

treatment_protocol: Peripheral blood was collected from all subjects directly into serum tubes before anti-viral treatment. The tubes were centrifuged at 1,500 g for 10 min at 4℃, sera were aliquoted and additionally centrifuged at 2,000 g to completely remove any remaining cells. Sera were stored at -80℃ until use.

tag: subject id

value: blood exosome

tag: extraction date

tag: gender

value: female

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs

tag: tg

tag: molecule subtype

value: microRNA


title: 22M

tag: disease

tag: agent


title: 7d_SS2_14681.30e [SLX-19435.i707_i517]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i729_i521]


title: HFFF cells infected with HSV-1 WT (17), 8hpi, PAA treated, histone H3, replicate 2

tag: infection


title: NL100

description: SAMPLE 67

tag: subject id

tag: extraction date

tag: gender

value: male

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt


title: NL98

description: SAMPLE 65

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs

tag: tg

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i706_i521]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 18M

tag: disease

tag: agent


title: 2w4w_SS2_146818.66b [SLX-20544.i728_i521]


title: NL99

description: SAMPLE 66

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast


title: 7d_SS2_14681.30e [SLX-19435.i706_i520]


title: 2w4w_SS2_146818.66b [SLX-20544.i727_i521]


title: NL96

description: SAMPLE 63

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs

tag: tg

tag: molecule subtype


title: 16M

tag: disease

tag: agent


title: NL95

description: SAMPLE 62

tag: subject id

tag: tissue

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)


title: 2w4w_SS2_146818.66b [SLX-20544.i716_i522]

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i726_i521]


title: 7d_SS2_14681.30e [SLX-19435.i706_i518]


title: 14M


title: NL92

description: SAMPLE 59

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb


title: 7d_SS2_14681.30e [SLX-19435.i706_i517]

tag: tissue


title: NL94

description: SAMPLE 61

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: alb

tag: bs

tag: tg

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i706_i516]

tag: cell type

tag: genotype

tag: treatment


title: 7d_SS2_14681.30e [SLX-19435.i706_i515]


title: NL93

description: SAMPLE 60

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc


title: 2w4w_SS2_146818.66b [SLX-20544.i723_i521]

tag: tissue


title: 2w4w_SS2_146818.66b [SLX-20544.i722_i521]


title: SS5-AS

description: rRNA-depleted RNA-seq of Arsenite-treated SH-SY5Y cell

treatment_protocol: SH-SY5Y cells were treated with 500 μM Sodium arsenite for 1 hr.

tag: cell line

value: neuroblastoma

value: 500 μM Sodium arsenite for 1 hr


title: 7d_SS2_14681.30e [SLX-19435.i706_i513]


title: NL91

description: SAMPLE 58

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb


title: 7d_SS2_14681.30e [SLX-19435.i705_i522]

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i721_i521]


title: 2w4w_SS2_146818.66b [SLX-20544.i724_i521]


title: 06M

tag: disease

tag: agent


title: 12M


title: 2w4w_SS2_146818.66b [SLX-20544.i720_i521]


title: NL90

description: SAMPLE 57

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: bs

tag: tg

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i719_i521]

tag: tissue


title: 11M


title: 7d_SS2_14681.30e [SLX-19435.i705_i521]

tag: cell type


title: 09M


title: NL89

description: SAMPLE 56

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb


title: NL88

description: SAMPLE 55

tag: hbsag

tag: anti-hcv

tag: ast


title: 08M

tag: disease

tag: agent


title: NL87

description: SAMPLE 54

tag: alt

tag: wbc

tag: bs

tag: tg

tag: molecule subtype


title: 07M


title: 2w4w_SS2_146818.66b [SLX-20544.i718_i521]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 7d_SS2_14681.30e [SLX-19435.i705_i520]


title: NL86

description: SAMPLE 53

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: plt

tag: alp

tag: ggtp


title: 2w4w_SS2_146818.66b [SLX-20544.i716_i521]


title: 02M

tag: disease

tag: agent


title: 7d_SS2_14681.30e [SLX-19435.i705_i517]


title: 2w4w_SS2_146818.66b [SLX-20544.i729_i520]


title: NL85

description: SAMPLE 52

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: hb

tag: alb

tag: bs

tag: tg

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i728_i520]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 01M


title: 7d_SS2_14681.30e [SLX-19435.i705_i518]


title: 7d_SS2_14681.30e [SLX-19435.i705_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i727_i520]


title: NL82

description: SAMPLE 49

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: plt

tag: alp

tag: ggtp


title: 7d_SS2_14681.30e [SLX-19435.i705_i513]


title: NL84

description: SAMPLE 51

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: hb

tag: alb

tag: bs


title: 2w4w_SS2_146818.66b [SLX-20544.i726_i520]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 95C

tag: disease

tag: agent


title: NL83

description: SAMPLE 50

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: plt

tag: tg

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i724_i520]


title: 90C


title: 89C


title: NL80

description: SAMPLE 47

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs


title: 7d_SS2_14681.30e [SLX-19435.i704_i521]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i723_i520]


title: 93C

tag: disease

tag: agent


title: NL79

description: SAMPLE 46

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: plt

tag: tg

tag: molecule subtype


title: 88C


title: NL78

description: SAMPLE 45

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs


title: 2w4w_SS2_146818.66b [SLX-20544.i722_i520]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i721_i520]


title: 7d_SS2_14681.30e [SLX-19435.i705_i516]


title: 7d_SS2_14681.30e [SLX-19435.i704_i518]


title: 84C

tag: disease

tag: agent


title: 86C


title: NL81

description: SAMPLE 48

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: plt

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i704_i517]


title: 2w4w_SS2_146818.66b [SLX-20544.i720_i520]


title: 2w4w_SS2_146818.66b [SLX-20544.i719_i520]


title: 7d_SS2_14681.30e [SLX-19435.i704_i522]


title: 83C


title: NL74

description: SAMPLE 41

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: tg


title: NL76

description: SAMPLE 43

tag: subject id

tag: tissue

tag: extraction date

tag: gender

tag: bs


title: NL75

description: SAMPLE 42

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: plt


title: 2w4w_SS2_146818.66b [SLX-20544.i718_i520]

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i716_i520]


title: 7d_SS2_14681.30e [SLX-19435.i704_i515]


title: 7d_SS2_14681.30e [SLX-19435.i704_i513]


title: 75C

tag: disease

tag: agent


title: NL73

description: SAMPLE 40

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i729_i518]

tag: tissue


title: 7d_SS2_14681.30e [SLX-19435.i703_i521]


title: 80C


title: 71C


title: 69C


title: 2w4w_SS2_146818.66b [SLX-20544.i727_i518]


title: NL72

description: SAMPLE 39

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: plt

tag: bs

tag: tg


title: NL70

description: SAMPLE 37

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc


title: 7d_SS2_14681.30e [SLX-19435.i703_i520]

tag: cell type

tag: genotype

tag: treatment


title: 68C

tag: disease

tag: agent


title: 2w4w_SS2_146818.66b [SLX-20544.i726_i518]

tag: tissue


title: 7d_SS2_14681.30e [SLX-19435.i703_i518]


title: NL71

description: SAMPLE 38

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: molecule subtype


title: NL69

description: SAMPLE 36

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: plt

tag: bs

tag: tg


title: 67C

tag: disease

tag: agent


title: NL68

description: SAMPLE 35

tag: subject id

tag: tissue

tag: extraction date

tag: gender

tag: age (yrs)

tag: wbc

tag: alp


title: 7d_SS2_14681.30e [SLX-19435.i703_i517]

tag: cell type

tag: genotype

tag: treatment


title: 66C


title: 7d_SS2_14681.30e [SLX-19435.i703_i522]


title: 2w4w_SS2_146818.66b [SLX-20544.i724_i518]


title: NL67

description: SAMPLE 34

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: ggtp

tag: hb

tag: alb

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i728_i518]

tag: tissue


title: 2w4w_SS2_146818.66b [SLX-20544.i723_i518]


title: 7d_SS2_14681.30e [SLX-19435.i703_i516]


title: 64C

tag: disease

tag: agent


title: 2w4w_SS2_146818.66b [SLX-20544.i722_i518]


title: NL66

description: SAMPLE 33

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: alt

tag: wbc

tag: plt

tag: alp

tag: bs

tag: tg


title: 7d_SS2_14681.30e [SLX-19435.i703_i513]

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i721_i518]


title: 62C


title: 61C


title: 2w4w_SS2_146818.66b [SLX-20544.i720_i518]


title: 57C


title: NL65

description: SAMPLE 32

tag: hbsag

tag: anti-hcv

tag: ast

tag: ggtp

tag: hb

tag: alb

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i702_i522]

tag: tissue


title: 7d_SS2_14681.30e [SLX-19435.i702_i521]


title: 2w4w_SS2_146818.66b [SLX-20544.i719_i518]


title: 2w4w_SS2_146818.66b [SLX-20544.i718_i518]


title: 51C

tag: disease

tag: agent


title: 7d_SS2_14681.30e [SLX-19435.i702_i520]


title: NL63

description: SAMPLE 30

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: alt

tag: wbc

tag: plt


title: 50C


title: 7d_SS2_14681.30e [SLX-19435.i703_i515]

tag: cell type

tag: genotype

tag: treatment


title: NL62

description: SAMPLE 29

tag: hbsag

tag: anti-hcv

tag: ast

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs

tag: tg

tag: molecule subtype


title: NL77

description: SAMPLE 44

tag: subject id

tag: tissue

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 7d_SS2_14681.30e [SLX-19435.i702_i518]

tag: cell type

tag: genotype

tag: treatment


title: 49C

tag: disease

tag: agent


title: NL64

description: SAMPLE 31

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb


title: 7d_SS2_14681.30e [SLX-19435.i702_i517]

tag: tissue


title: 48C


title: 2w4w_SS2_146818.66b [SLX-20544.i729_i517]


title: NL60

description: SAMPLE 27

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: bs

tag: tg

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i727_i517]

tag: cell type

tag: genotype

tag: treatment


title: NL61

description: SAMPLE 28

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alp

tag: ggtp


title: 7d_SS2_14681.30e [SLX-19435.i702_i513]

tag: tissue


title: 2w4w_SS2_146818.66b [SLX-20544.i716_i518]


title: 44C

tag: disease

tag: agent


title: 2w4w_SS2_146818.66b [SLX-20544.i726_i517]


title: 42C


title: 47C


title: 40C


title: 2w4w_SS2_146818.66b [SLX-20544.i724_i517]


title: 7d_SS2_14681.30e [SLX-19435.i701_i522]


title: 10M


title: NL55

description: SAMPLE 23

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hb

tag: alb

tag: bs


title: NL56

description: SAMPLE 24

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: tg

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i701_i521]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 7d_SS2_14681.30e [SLX-19435.i702_i516]


title: 2w4w_SS2_146818.66b [SLX-20544.i722_i517]


title: 7d_SS2_14681.30e [SLX-19435.i702_i515]


title: NL58

description: SAMPLE 25

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: plt

tag: alp

tag: ggtp


title: NL59

description: SAMPLE 26

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: hb

tag: alb

tag: bs


title: 7d_SS2_14681.30e [SLX-19435.i701_i520]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 37C

tag: disease

tag: agent


title: 2w4w_SS2_146818.66b [SLX-20544.i721_i517]


title: NL52

description: SAMPLE 20

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: alt

tag: wbc

tag: plt

tag: tg

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i701_i517]


title: NL53

description: SAMPLE 21

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs


title: 2w4w_SS2_146818.66b [SLX-20544.i723_i517]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: NL54

description: SAMPLE 22

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: alt

tag: wbc

tag: plt


title: 38C

tag: disease

tag: agent


title: 36C


title: 34C


title: 2w4w_SS2_146818.66b [SLX-20544.i719_i517]


title: NL51

description: SAMPLE 19

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alp

tag: ggtp

tag: hb

tag: tg

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i718_i517]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 31C


title: 27C


title: 7d_SS2_14681.30e [SLX-19435.i701_i515]


title: 7d_SS2_14681.30e [SLX-19435.i701_i513]


title: 2w4w_SS2_146818.66b [SLX-20544.i716_i517]


title: 7d_SS2_14681.30e [SLX-19435.i701_i518]


title: 2w4w_SS2_146818.66b [SLX-20544.i720_i517]


title: 2w4w_SS2_146818.66b [SLX-20544.i729_i516]


title: 26C


title: NL47

description: SAMPLE 15

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: alt

tag: wbc

tag: plt

tag: alb

tag: bs


title: 7d_SS2_14681.32c [SLX-19435.i729_i511]


title: 7d_SS2_14681.30e [SLX-19435.i701_i516]


title: NL50

description: SAMPLE 18

tag: hbsag

tag: anti-hcv

tag: ast

tag: alp

tag: ggtp

tag: hb


title: 7d_SS2_14681.32c [SLX-19435.i729_i510]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 25C

tag: disease

tag: agent


title: 23C


title: NL48

description: SAMPLE 16

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: alt

tag: tg

tag: molecule subtype


title: NL49

description: SAMPLE 17

tag: hbsag

tag: anti-hcv

tag: ast

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: alb

tag: bs


title: 2w4w_SS2_146818.66b [SLX-20544.i728_i516]

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: 7d_SS2_14681.32c [SLX-19435.i729_i508]


title: NL45

description: SAMPLE 13

tag: subject id

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: alt


title: 2w4w_SS2_146818.66b [SLX-20544.i727_i516]


title: 7d_SS2_14681.32c [SLX-19435.i729_i507]


title: 22C

tag: disease

tag: agent


title: 2w4w_SS2_146818.66b [SLX-20544.i726_i516]


title: 21C


title: 20C


title: 2w4w_SS2_146818.66b [SLX-20544.i724_i516]


title: 7d_SS2_14681.32c [SLX-19435.i729_i506]


title: 2w4w_SS2_146818.66b [SLX-20544.i723_i516]


title: 7d_SS2_14681.32c [SLX-19435.i729_i505]


title: 78C


title: NL46

description: SAMPLE 14

tag: hbsag

tag: anti-hcv

tag: ast

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: tg

tag: molecule subtype


title: NL43

description: SAMPLE 11

tag: subject id

tag: tissue

tag: extraction date

tag: gender

tag: age (yrs)

tag: alb

tag: bs


title: NL44

description: SAMPLE 12

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: alt


title: 18C

tag: disease

tag: agent


title: 7d_SS2_14681.32c [SLX-19435.i729_i503]

tag: cell type

tag: genotype

tag: treatment


title: 17C


title: 2w4w_SS2_146818.66b [SLX-20544.i722_i516]


title: 7d_SS2_14681.32c [SLX-19435.i729_i502]


title: NL42

description: SAMPLE 10

tag: subject id

tag: anti-hcv

tag: ast

tag: wbc

tag: plt

tag: alp

tag: ggtp

tag: hb

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i704_i516]

tag: tissue


title: 7d_SS2_14681.30e [SLX-19435.i728_i511]


title: NL41

description: SAMPLE 9

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: alb


title: 2w4w_SS2_146818.66b [SLX-20544.i720_i516]

tag: cell type

tag: genotype

tag: treatment


title: NL38

description: SAMPLE 7

tag: subject id

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: plt

tag: bs

tag: tg


title: 2w4w_SS2_146818.66b [SLX-20544.i721_i516]

tag: tissue


title: NL39

description: SAMPLE 8

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: alp

tag: ggtp

tag: hb

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i728_i510]

tag: cell type

tag: genotype

tag: treatment


title: 14C

tag: disease

tag: agent


title: 16C


title: 2w4w_SS2_146818.66b [SLX-20544.i719_i516]


title: 11C


title: 7d_SS2_14681.30e [SLX-19435.i728_i507]


title: NL37

description: SAMPLE 6

tag: subject id

value: ND

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alb


title: 2w4w_SS2_146818.66b [SLX-20544.i718_i516]

tag: tissue


title: NL35

description: SAMPLE 4

tag: extraction date

tag: gender

tag: age (yrs)

tag: height (cm)

tag: alp

tag: ggtp

tag: hb

tag: bs

tag: tg

tag: molecule subtype


title: 7d_SS2_14681.30e [SLX-19435.i728_i508]

tag: cell type

tag: genotype

tag: treatment


title: 7d_SS2_14681.30e [SLX-19435.i728_i506]


title: 2w4w_SS2_146818.66b [SLX-20544.i716_i516]


title: 7d_SS2_14681.30e [SLX-19435.i728_i505]


title: 09C

tag: disease

tag: agent


title: 08C


title: 15C


title: 07C


title: 02C


title: 7d_SS2_14681.30e [SLX-19435.i728_i503]


title: NL36

description: SAMPLE 5

tag: subject id

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv

tag: ast

tag: alt

tag: wbc

tag: plt

tag: alb


title: 01C


title: 7d_SS2_14681.32c [SLX-19435.i727_i511]

tag: tissue


title: 2w4w_SS2_146818.66b [SLX-20544.i729_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i724_i515]


title: HCC28

description:
SAMPLE 45
microRNA in blood exosome of HCC patients

source_name: HCC patient

tag: subject status/id

value: HCC patient 27

tag: age

tag: gender

tag: afp

tag: dcp

tag: cea

value: NT

value: peripheral blood

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i727_i515]

value: bone marrow

tag: cell type

tag: genotype

tag: treatment


title: 2w4w_SS2_146818.66b [SLX-20544.i726_i515]

value: Lin-negative, (cKit OR Sca1)-positive


title: 7d_SS2_14681.32c [SLX-19435.i727_i510]

value: WT


title: HCC27

description:
SAMPLE 44
microRNA in blood exosome of HCC patients

value: HCC patient 26

tag: hbsag

tag: anti-hcv


title: 2w4w_SS2_146818.66b [SLX-20544.i728_i515]


title: HCC26

description:
SAMPLE 43
microRNA in blood exosome of HCC patients

value: HCC patient 25


title: 7d_SS2_14681.32c [SLX-19435.i727_i508]


title: NL30

description: SAMPLE 1

tag: subject id

tag: extraction date

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: ast

tag: alt

tag: alp

tag: ggtp

tag: hb

tag: bs

tag: tg


title: NL32

description: SAMPLE 2

tag: tissue

tag: gender

tag: wbc

tag: plt

tag: alb

tag: molecule subtype


title: 2w4w_SS2_146818.66b [SLX-20544.i728_i517]

tag: cell type

tag: genotype

tag: treatment


title: NL34

description: SAMPLE 3

tag: subject id

tag: extraction date

tag: age (yrs)

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: hbsag

tag: anti-hcv


title: Mouse_APAP_24h_5

city: Liverpool

first: Ian

last: Copple

address: Ashton Street

department: Department of Pharmacology and Therapeutics

institute: University of Liverpool

description: Gene expression data from liver of mice treated with 300 mg/kg APAP at 24h after administration

hyb_protocol: Following fragmentation, 30 µg of cRNA were hybridized for 16h at 45°C on Affymetrix GeneChip™ Mouse Genome 430 2.0 Array or GeneChip™ Rat Genome 230 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Quality control and low level analysis of raw fluorescence intensities was performed using the affy package (v1.64.0) in R v3.6.1. Raw data were processed using RMA normalization and a custom chip-definition file (CDF version 24 for mouse and version 19 for rat) from the BrainArray (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp) resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated microarray probes to 18,180 and 13,877 genes for mouse and rat, respectively. Differential expression analyses were carried out using the limma package (v3.42.2) in R.

label: biotin

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA.

extract_protocol: Frozen liver samples were homogenised in Qiazol Lysis Reagent (Qiagen), and total RNA was purified following the manufacturer’s instructions.

tag: tissue

value: liver

tag: strain

tag: Sex

value: 300 mg/kg acetamnophen (o.g.)

tag: hours after treatment


title: Mouse_APAP_24h_4


title: Mouse_APAP_24h_3


title: 2w4w_SS2_146818.66b [SLX-20544.i721_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i722_i515]


title: 7d_SS2_14681.32c [SLX-19435.i727_i507]


title: 2w4w_SS2_146818.66b [SLX-20544.i723_i515]


title: HCC17

description:
SAMPLE 39
microRNA in blood exosome of HCC patients

tag: subject status/id

value: HCC patient 21

tag: age

tag: gender

tag: afp

tag: dcp

tag: cea


title: HCC18

description:
SAMPLE 40
microRNA in blood exosome of HCC patients

value: HCC patient 22

tag: molecule subtype


title: HCC20

description:
SAMPLE 41
microRNA in blood exosome of HCC patients

value: HCC patient 23

value: microRNA


title: 7d_SS2_14681.30e [SLX-19435.i728_i502]

tag: cell type

tag: genotype

tag: treatment


title: HCC25

description:
SAMPLE 42
microRNA in blood exosome of HCC patients

value: HCC patient 24

value: male


title: 2w4w_SS2_146818.66b [SLX-20544.i720_i515]


title: 7d_SS2_14681.32c [SLX-19435.i727_i506]


title: 7d_SS2_14681.32c [SLX-19435.i727_i505]


title: 2w4w_SS2_146818.66b [SLX-20544.i719_i515]


title: 2w4w_SS2_146818.66b [SLX-20544.i718_i515]


title: 7d_SS2_14681.30e [SLX-19435.i704_i520]


title: 7d_SS2_14681.32c [SLX-19435.i727_i503]


title: Mouse_APAP_24h_1


title: HCC15

description:
SAMPLE 37
microRNA in blood exosome of HCC patients

value: HCC patient 19


title: 2w4w_SS2_146818.66b [SLX-20544.i716_i515]


title: Mouse_APAP_24h_2


title: Mouse_APAP_09h_5

description: Gene expression data from liver of mice treated with 300 mg/kg APAP at 9h after administration


title: Mouse_APAP_09h_4


title: HCC14

description:
SAMPLE 36
microRNA in blood exosome of HCC patients

value: HCC patient 18


title: HCC13

description:
SAMPLE 35
microRNA in blood exosome of HCC patients

value: HCC patient 17

value: NT


title: 7d_SS2_14681.30e [SLX-19435.i726_i511]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX19435_scB5Tom_7d_ss2_fcounts.txt

value: bone marrow


title: 2w4w_SS2_146818.66b [SLX-20544.i729_i513]

value: Lin-negative, (cKit OR Sca1)-positive


title: 2w4w_SS2_146818.66b [SLX-20544.i728_i513]

value: WT


title: 7d_SS2_14681.30e [SLX-19435.i726_i510]


title: 7d_SS2_14681.30e [SLX-19435.i726_i508]


title: 2w4w_SS2_146818.66b [SLX-20544.i727_i513]


title: HCC12

description:
SAMPLE 34
microRNA in blood exosome of HCC patients

value: HCC patient 16

value: female

value: peripheral blood


title: Mouse_APAP_09h_3

value: liver

value: 300 mg/kg acetamnophen (o.g.)


title: HCC11

description:
SAMPLE 33
microRNA in blood exosome of HCC patients

value: HCC patient 15


title: 7d_SS2_14681.30e [SLX-19435.i726_i507]


title: 2w4w_SS2_146818.66b [SLX-20544.i724_i513]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20544_scB5Tom_2w_ss2_fcounts.txt


title: 7d_SS2_14681.32c [SLX-19435.i727_i502]


title: 2w4w_SS2_146818.66b [SLX-20544.i726_i513]


title: Mouse_APAP_09h_1


title: HCC9

description:
SAMPLE 31
microRNA in blood exosome of HCC patients

value: HCC patient 13


title: Mouse_APAP_09h_2


title: 2w4w_SS2_146818.66b [SLX-20544.i723_i513]


title: 7d_SS2_14681.30e [SLX-19435.i726_i505]


title: Mouse_APAP_06h_4

description: Gene expression data from liver of mice treated with 300 mg/kg APAP at 6h after administration


title: Mouse_APAP_06h_3


title: HCC8

description:
SAMPLE 30
microRNA in blood exosome of HCC patients

value: HCC patient 12

value: microRNA


title: 7d_SS2_14681.30e [SLX-19435.i726_i502]


title: 2w4w_SS2_146818.66b [SLX-20544.i721_i513]


title: Mouse_APAP_06h_5

value: male


title: HCC16

description:
SAMPLE 38
microRNA in blood exosome of HCC patients

value: HCC patient 20


title: HCC6

description:
SAMPLE 28
microRNA in blood exosome of HCC patients

value: HCC patient 10


title: HCC5

description:
SAMPLE 27
microRNA in blood exosome of HCC patients

value: HCC patient 9


title: 7d_SS2_14681.30e [SLX-19435.i726_i506]


title: 2w4w_SS2_146818.66b [SLX-20544.i720_i513]


title: 7d_SS2_14681.32c [SLX-19435.i724_i510]


title: 2w4w_SS2_146818.66b [SLX-20544.i719_i513]


title: 7d_SS2_14681.32c [SLX-19435.i724_i511]


title: Mouse_APAP_06h_2


title: 2w4w_SS2_146818.66b [SLX-20544.i722_i513]


title: Mouse_APAP_03h_5

description: Gene expression data from liver of mice treated with 300 mg/kg APAP at 3h after administration


title: 7d_SS2_14681.30e [SLX-19435.i726_i503]


title: HCC4

description:
SAMPLE 26
microRNA in blood exosome of HCC patients

value: HCC patient 8

value: NT


title: 2w4w_SS2_146818.66b [SLX-20544.i718_i513]

value: bone marrow

value: Lin-negative, (cKit OR Sca1)-positive


title: Mouse_APAP_06h_1


title: 7d_SS2_14681.32c [SLX-19435.i724_i508]

value: WT


title: HCC3

description:
SAMPLE 25
microRNA in blood exosome of HCC patients

value: HCC patient 7


title: 2w4w_SS2_146818.66b [SLX-20544.i716_i513]


title: Mouse_APAP_03h_2


title: 7d_SS2_14681.32c [SLX-19435.i724_i507]


title: HCC2

description:
SAMPLE 24
microRNA in blood exosome of HCC patients

value: HCC patient 6

value: peripheral blood


title: HCC7

description:
SAMPLE 29
microRNA in blood exosome of HCC patients

value: HCC patient 11

value: female


title: 7d_SS2_14681.32c [SLX-19435.i724_i506]


title: Mouse_APAP_03h_4

value: liver

value: 300 mg/kg acetamnophen (o.g.)


title: 2w4w_SS2_146818.66b [SLX-20544.i714_i522]


title: HCC1

description:
SAMPLE 23
microRNA in blood exosome of HCC patients

value: HCC patient 5

value: microRNA


title: 2w4w_SS2_146818.66b [SLX-20544.i715_i522]


title: HCC-OC-004-1

description:
SAMPLE 22
microRNA in blood exosome of HCC patients

value: HCC patient 4


title: 7d_SS2_14681.32c [SLX-19435.i724_i505]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX19435_scB5Tom_7d_ss2_fcounts.txt


title: 7d_SS2_14681.32c [SLX-19435.i724_i503]


title: HCC-OC-003-1

description:
SAMPLE 21
microRNA in blood exosome of HCC patients

value: HCC patient 3

value: male


title: 2w4w_SS2_146818.66b [SLX-20544.i712_i522]


title: Mouse_APAP_03h_3


title: Mouse_APAP_03h_1


title: Mouse_Vehicle_24h_4

description: Gene expression data from liver of mice treated with vehicle at 24h after administration

value: Vehicle (1% [w/v] hydroxyethylcellulose, o.g.)


title: Mouse_Vehicle_24h_5


title: HCC-OC-002-1

description:
SAMPLE 20
microRNA in blood exosome of HCC patients

value: HCC patient 2


title: 2w4w_SS2_146818.66b [SLX-20544.i711_i522]

description:
Smart-Seq2 scRNA-Seq, see metadata for details
SLX20544_scB5Tom_2w_ss2_fcounts.txt

value: bone marrow


title: 7d_SS2_14681.32c [SLX-19435.i724_i502]

value: Lin-negative, (cKit OR Sca1)-positive


title: Mouse_Vehicle_24h_2


title: 2w4w_SS2_146818.66b [SLX-20544.i710_i522]

value: WT


title: HCC-OC-001-1

description:
SAMPLE 19
microRNA in blood exosome of HCC patients

value: HCC patient 1


title: Mouse_Vehicle_24h_3


title: 2w4w_SS2_146818.66b [SLX-20544.i707_i522]


title: 7d_SS2_14681.30e [SLX-19435.i723_i510]


title: 2w4w_SS2_146818.66b [SLX-20544.i706_i522]


title: OCU-CH107

description:
SAMPLE 18
microRNA in blood exosome of CHC patients

source_name: CHC patient

value: CHC patient 4

value: NT


title: 7d_SS2_14681.30e [SLX-19435.i723_i511]


title: Mouse_Vehicle_24h_1


title: 7d_SS2_14681.30e [SLX-19435.i723_i507]


title: 7d_SS2_14681.30e [SLX-19435.i723_i508]


title: Mouse_Vehicle_09h_5

description: Gene expression data from liver of mice treated with vehicle at 9h after administration


title: OCU-CH106

description:
SAMPLE 17
microRNA in blood exosome of CHC patients

value: CHC patient 3

value: peripheral blood


title: Mouse_Vehicle_09h_3

value: liver