title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 3 [14D_CTRL_3]


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 4 [14D_CTRL_4]

status: Public on Dec 10 2023

type: RNA

city: Warsaw

first: Kinga

last: Szydlowska

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

description: Gene expression data from plasma of adult rats after amygdala stimulation

hyb_protocol: Hybridization was done for 20 hours in +48 °C (AF-900454 GeneChip Hybridization Control Kit, Affymetrix). It was followed by the wash and stain protocol (AF-901910 FlashTagTM Biotin HSR RNA Labeling Kit, Affymetrix). The whole procedure was performed using GeneAtlas™ instrument from Affymetrix (#00-0393).

scan_protocol: The whole procedure was performed using GeneAtlas™ instrument from Affymetrix.

data_processing: Data analysis of the miRNA 4.1 Array Strips identifying up- and down-regulated miRNAs was performed with RStudio (R v. 3.3.2) using Bioconductor (Gentleman et al. 2004, R_Core_Team 2012), oligo and limma (G 2005) packages. The microarray data were normalized with the Robust Multi-array Average (RMA) algorithm (oligo package version 1.22.0) (Carvalho and Irizarry 2010). For the expression analysis, the calculated p-values were based on moderated t-statistics. Furthermore, the Benjamini and Hochberg multiple testing adjustment method was applied to the p-values (FDR – False Discovery Rate). A one-way ANOVA was used to establish  miRNA with differential levels between the tested groups.  The correlation, unsupervised clustering and PCA (principal component analyses) were performed in the RStudio (R version 3.3.2) (R_Core_Team 2012). PCA was performed on microarray probes using package stats and the lattice package (Sakar D 2008). For the heatmap clustering of miRNAs with significantly different level (p < 0.05), miRNAs were ordered with the clustering complete-linkage method, together with the Pearson correlation distance measure. The heatmap diagrams were generated with the gplots package (Warnes GR 2012). Pearson correlation test was used to analyze the correlations between miRNAs with significantly different level (p < 0.05) between stimulated and sham-operated control animals. The fuzzy c-means algorithm implemented in the Mfuzz package (Kumar & E Futschik, 2007) was used to perform clusterization on all probes.  Data analysis of the miRNA 4.1 Array Strips identifying up- and down-regulated miRNAs was performed with RStudio (R v. 3.3.2) using Bioconductor (Gentleman et al. 2004, R_Core_Team 2012), oligo and limma (G 2005) packages. The microarray data were normalized with the Robust Multi-array Average (RMA) algorithm (oligo package version 1.22.0) (Carvalho and Irizarry 2010). For the expression analysis, the calculated p-values were based on moderated t-statistics. Furthermore, the Benjamini and Hochberg multiple testing adjustment method was applied to the p-values (FDR – False Discovery Rate). A one-way ANOVA was used to establish  miRNA with differential levels between the tested groups.  The correlation, unsupervised clustering and PCA (principal component analyses) were performed in the RStudio (R version 3.3.2) (R_Core_Team 2012). PCA was performed on microarray probes using package stats and the lattice package (Sakar D 2008). For the heatmap clustering of miRNAs with significantly different level (p < 0.05), miRNAs were ordered with the clustering complete-linkage method, together with the Pearson correlation distance measure. The heatmap diagrams were generated with the gplots package (Warnes GR 2012). Pearson correlation test was used to analyze the correlations between miRNAs with significantly different level (p < 0.05) between stimulated and sham-operated control animals. The fuzzy c-means algorithm implemented in the Mfuzz package (Kumar & E Futschik, 2007) was used to perform clusterization on all probes.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: adult, male rat

label_protocol: miRNA level was profiled using miRNA 4.1 Array Strip (#902404, Santa Clara, CA, Affymetrix). Procedure was performed according to manufacturer’s recommendations. 8 µl of RNA was used to perform poly-A-tailing reaction (AF-902134 GA HWS Kit for miRNA Arrays, Affymetrix).

growth_protocol: Adult, male Sprague-Dawley rats (270-320 g) from Mossakowski Medical Research Centre Polish Academy of Sciences, in Warsaw (Poland) were used in this study. Rats were housed under controlled conditions (24 °C, humidity 50 - 60 %, 12/12 h light-dark cycle) with food and water available ad libitum. Animals were housed in pairs. Environment was enriched by using various toys (wooden or plastic balls, wooden bridges, etc.) and snacks, which were changed every week. Starting four weeks before electrical stimulation rats were subjected to regular handling every other day for 10 minutes.

extract_protocol: Blood drawn from rat tail vein was drawn at 4 time points and cecntrifuged to separate plasma. miRNA was isolated from 50 µl of plasma using miRCURY kit from Qiagen. The whole miRNA isolation procedure was performed as described by the kit manufacturer. In the end of the procedure RNA was eluted to 50 µl of RNAse free water, aliquoted and stored in -80°C.

treatment_protocol: The amygdala stimulation model of temporal lobe epilepsy was used in this study as previously described with some modifications (Guzik-Kornacka et al, 2011; Nissinen et al., 2000). Surgery was performed under isoflurane anesthesia (2-2.5 % in 100 % O2) followed by the injection of butorphanol (Butomidor, Richter Pharma AG, Wells, Austria; 0.5 mg/kg i.p.) for analgesia. A stimulating and recording bipolar wire electrode (Plastic One Inc., Roanoke, VA, # E363-3-2WT-SPC) was implanted into the left lateral nucleus of the amygdala 3.6 mm posterior and 5.0 mm lateral to bregma, 6.5 mm ventral to the surface of the brain. A stainless steel screw electrode (Plastic One Inc., Roanoke, VA, #E363/20) was implanted contralaterally into the skull over the right frontal cortex (3.0 mm anterior and 2.0 mm lateral to bregma) as a surface EEG recording electrode. Two stainless steel screw electrodes were placed bilaterally over the cerebellum (10.0 mm posterior and 2.0 mm lateral to bregma) as grounding and reference electrodes. The contacts of all electrodes were placed in a multi-channel electrode pedestal (Plastic One Inc., Roanoke, VA, #MS363) which was attached to the skull with dental acrylate (Duracryl Plus). After two weeks of recovery, animals were electrically stimulated via the intra-amygdala electrode to evoke status epilepticus. Stimulation consisted of a 100-ms train of 1-ms biphasic square-wave pulses (400 μA peak to peak) delivered at 60 Hz every 0.5 s for 30 min. If the animal did not enter status epilepticus, stimulation was continued for an additional 10 min. The status epilepticus was stopped 1 h after stimulation via an intraperitoneal injection of diazepam (20 mg/kg). If the first dose of diazepam did not suppress status epilepticus , the animal received subsequent doses of diazepam at   5 mg/kg. Time matched control animals had electrodes implanted but did not receive electrical stimulation (sham animals).

tag: strain

value: Sprague Dawley

tag: age

value: adult

tag: Sex

value: male

tag: blood collection tube coating

value: tubes coated with 1 mg K2EDTA #363706 BD Vacutainer

tag: tissue

value: plasma

tag: time point

tag: molecule subtype

value: miRNA

tag: subdivision of stimulated animals based on seizure number

value: CTRL

tag: subdivision of stimulated animals based on epilepsy development at given time point

tag: subdivision of stimulated animals based on time of epilepsy developmentepilepsy development


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 2 [14D_CTRL_2]


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 1 [14D_CTRL_1]


title: NST7B_CD3Neg

type: SRA

city: San Francisco

first: Margaret

last: Lowe

state: CA

address: 513 Parnassus Avenue, HSW1201B

country: USA

institute: UCSF

library_source: transcriptomic single cell

data_processing:
Fastq files were analyzed with Cell Ranger Version 3.0.2
Assembly: GRCh38
Supplementary files format and content: filtered feature bc matrices

molecule: polyA RNA

organism: Homo sapiens

source_name: blood from healthy donor

extract_protocol:
Cells were purified as live, CD45+, CD3- from skin that was enzymatically digested overnight with collagenase IV in the presence of DNAse.
sRNASeq was performed using the 10x Single Cell 5’ Chemistry

value: blood from healthy donor

tag: cell type

value: CD3 Negative Immune Cells


title: TCZ_Baseline_3400

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

hyb_protocol: Equimolar target/reference mixes were hybridised to custom Agilent 60-mer arrays (EPI_8X60_3P_004; Epistem) according to the manufacturer's instructions.

scan_protocol: Slides were scanned for Cy5 and Cy3 on an Agilent Technologies Microarray Scanner G2505c (Serial number US91903684) at a 3uM resolution producing a 20Bit tiff image. Array data was extracted from the scanned images using the default Agilent 2 colour extraction protocol GE2_105_Dec08 in Agilent feature extraction version 10.5.1.

data_processing: Preprocessing of the probe set intensities included background correction, normalisation (Loess), and replicate averaging, excluding control probes and feature filtering (removal of features not associated with a Gene ID and duplicate Gene IDs).

source_name: reference

label_protocol: Individual cDNA test samples were labelled with Cy5 and an equimolar pool of all amplified cDNA samples was used to incorporate Cy3 fluorophore using an RNAamp Cy3/Cy5 labelling kit (Epistem).

growth_protocol: RNA amplification was performed using 10 ng total RNA and the RNAamp RNA Nano amplification kit (Epistem, Manchester, UK). Amplified cDNA was assessed quantitatively (NanoDrop) and qualitatively (Bioanalyzer; Agilent).

extract_protocol: Skin samples were homogenised in TRIzol (ThermoFisher Scientific, Waltham, MA, USA) using a polytron homogeniser, and total RNA was isolated according to the manufacturer's protocol.

tag: sample type

value: reference

source_name: test

value: skin biopsy

tag: disease state

value: SSc

tag: subject

tag: treatment

value: Tocilizumab

value: Baseline

tag: mrss


title: NST10B_CD3Neg


title: TCZ_Baseline_3401


title: NST8B_CD3Neg


title: PBO_Baseline_2401

value: Placebo


title: HNV_Control_3

value: Healthy

value: Control


title: PBO_Baseline_2400


title: NST5B_CD3Neg


title: NST10_CD3Neg

source_name: skin from healthy donor

value: skin from healthy donor


title: PBO_Baseline_3301


title: TCZ_Baseline_2200


title: PBO_Baseline_2201


title: TCZ_Baseline_3300


title: TCZ_Baseline_3200


title: TCZ_Baseline_3201


title: NST9_CD3Neg


title: NST8_CD3Neg


title: HNV_Control_2


title: NST5_CD3Neg


title: NST7_CD3Neg


title: PBO_Baseline_2300


title: HNV_Control_20


title: HNV_Control_19


title: HNV_Control_18


title: HS10x6B_CD3Neg

source_name: blood from HS patient

value: blood from HS patient


title: PBO_Baseline_1603


title: HNV_Control_17


title: HNV_Control_16


title: HS10x5B_CD3Neg


title: HS10x2_CD3Neg

source_name: skin from HS lesion

value: skin from HS lesion


title: HS419_CD3Neg


title: TCZ_Baseline_1600


title: HS10x4_CD3Neg


title: HS10x6_CD3Neg


title: HS10x5_CD3Neg


title: HS419B_CD3Neg


title: MCF10A_EXO

city: Xiamen City

first: Yuting

last: Lin

state: -- Please Select --

address: Xiamen University, Xiang'an District, Xiamen City, Fujian Province, China

country: China

institute: XIAMEN UNIVERSITY

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/ low-quality sequence using fastp (0.19.5).
Trimmed sequence reads were mapped to GRCh38.p13 (MCF10A) or GRCm39 (NMuMG) using HISAT2（http://ccb.jhu.edu/software/hisat2/index.shtml）.
Using the alignment results to the genome and genome annotation file, RSEM was employed to obtain read counts for each gene in the samples. Subsequently, the read counts were transformed into Transcripts Per Million (TPM) to achieve standardized gene expression levels.
Assembly: GRCh38.p13; GRCm39
Supplementary files format and content: Excel files include TPM values for each Sample

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). >1 ug of total RNA was used for the construction of sequencing libraries.
The RNA libraries for RNA-seq were prepared using Illumina TruSeq™ RNA sample prep kit following the manufacturer's protocols.

tag: cell line

value: mammary epithelial cells

tag: genotype

value: WT

value: CDEs-treated


title: MCF10AKO

value: CREPT knockout

value: PBS-treated


title: HS10x2B_CD3Neg

value: CD3 Negative Immune Cells


title: HNV_Control_14

value: reference


title: MCF10AKO_EXO


title: HS10x4B_CD3Neg


title: HNV_Control_12

value: skin biopsy


title: HNV_Control_10


title: Cut-Tag-AP2XII-1-CTL-2

city: Nanning

first: Dandan

last: Hu

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

library_source: genomic

data_processing:
The RNA-SEQ Paired-end clean reads were aligned to the reference genome using Hisat2. Read counts for each gene were calculated using the sorted bam files using StringTie. Differentially expressed genes (DEGs) between treated and untreated parasites were calculated by edgeR.
For cut&tag peak calling, the paired-end reads were filtered and then aligned to the T. gondii reference genome using Bowtie2 (v.2.1.0). The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Sambamba. The filtered reads were then employed to identify Cut-Tag peaks using MACS2. The overlapped peaks in two biological replicates were identified by the Irreproducibility Discovery Rate (IDR). The final peaks were annotated against the latest T. gondii data in ToxoDB.
Assembly: reference genome of Toxoplasma Type II ME49 strain (ToxoDB-57)
Supplementary files format and content: .count files are the raw read count files of RNA-SEQ data. .bw files are the bigwig files for the cut&tag peaks.

molecule: genomic DNA

organism: Toxoplasma gondii

source_name: T. gondii

extract_protocol:
Total RNAs from T. gondii tachyzoites were then extracted using the M5 Total RNA Extraction Reagent (Mei5 Biotechnology Co., Ltd, Beijing) according to the manufacturer’s protocol. Cut&tag DNA extraction was performed using DNA extract beads (Vazyme, Jiangsu, China)
RNA-SEQ libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations. Cut&tag libraries were generated by PCR amplification with specific adaptors according to the manufacturer’s recommendations (TruePrep Index Kit V4 for Illumina, Vazyme, Nanjing, China)
RNA-SEQ; CUT&TAG

value: T. gondii

value: RH

value: untreated


title: PBO_Baseline_1601

value: SSc

value: Placebo

value: Baseline


title: HNV_Control_13

value: Healthy

value: Control


title: HNV_Control_15


title: HNV_Control_1


title: HNV_Control_11


title: SRSF5 iCLIP2 no UV control

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

data_processing:
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with non-default parameters: flexbar --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcode.fasta
Mapping: STAR (v2.7.3a) with non-default parameters: STAR --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 76 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate (output: SAMPLE.mapped.bam)
Remove reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): Samtools (v1.9), bedtools (v2.27.1): samtools view -H SAMPLE.mapped.bam > SAMPLE.header; samtools view SAMPLE.mapped.bam > SAMPLE.body; bedtools bamtobed -i SAMPLE.mapped.bam | sort -k1,1 > SAMPLE.mapped.bed; join -t $'\t' -j1 -e "NA" -a1 SAMPLE.mapped.bed CHROMOLENGTHTABLE > SAMPLE.mapped.len.bed; cat SAMPLE.mapped.len.bed | awk '{if(($2==0) || ($3>=$7)) printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6;}' > SAMPLE.idlist; awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.idlist SAMPLE.body > SAMPLE.body.filtered; cat SAMPLE.header SAMPLE.body.filtered | samtools view -b - > SAMPLE.bam
Duplicate removal: UMI-tools (v1.0.0) with non-default parameters: umi_tools dedup -I SAMPLE.bam -S SAMPLE.duprm.bam --method unique
BAM to BED shifting one base upstream: bedtools (v2.27.1): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.27.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
Assembly: GRCh38.p12 (Gencode release 31)
Supplementary files format and content: BW files containing the genomic coordinates and counts of uniquely mapped X-links for each replicate separated by strand.

source_name: HeLa

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and penicilin/streptomycin antibiotics at 37˚C with 5% CO2 and 21% oxygen.

extract_protocol:
Cells were lysed and treated with RNase I. SRSF5 was immunoprecipitated with Gamma binding beads coupled to anti-GFP antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer and a second adapter containing a barcode was ligated to the cDNAs. The cDNA was pre-amplified for 6 cycles using short Solexa P3 and P7 primers. After a size selection on beads a second PCR amplification was performed with the normal P3 and P7 primers to generate the final iCLIP2 libraries.
iCLIP2

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

value: HeLa

value: HeLa hGRAD SRSF5-GFP-endo

tag: rip antibody

value: anti-GFP antibody

tag: barcode sequence

value: NNNNNCTGATCNNNN

tag: fraction

value: SRSF5-bound RNA


title: SRSF5 iCLIP2 Replicate 5

value: NNNNNTGACATNNNN


title: MCF10A

value: mammary epithelial cells

value: WT

value: PBS-treated


title: PBO_Baseline_1300

value: reference

tag: tissue

value: skin biopsy


title: RNASEQ_GFP_control_biorep_3

city: Champaign

first: Pablo

last: Pinera

state: Illinois

address: 2332 West John Street, Apt. D

department: Bioengineering

institute: University of Illinois at Urbana-Champaign

data_processing:
For RNA-seq, FASQC was used for quality check filtering reqd quality scores below 30, reads mapped with HISAT2 and counted across aligned genome with featureCounts. DEG analysis performed with limma-voom, which filtered gened with a conts-per-million value below 0.5
Assembly: chr38
Supplementary files format and content: RNA-seq, .csv files are provided in "Processed GEO data.csv" with logFC expression for all genes as well as counts-per-million values for genes of interest in desired KEGG pathways

source_name: kidney

extract_protocol: RNeasy RNA extraction ployA library prep with TruSeq mRNA library prep, sequenced with NovaSeq 6000

value: kidney

value: epithelial

value: Lipofectamine 2000 transfected GFP Plasmid


title: RNASEQ_GFP_control_biorep_2


title: SRSF5 iCLIP2 Replicate 4

value: NNNNNTTGACTNNNN


title: RNASEQ_GFP_control_biorep_1


title: Cut-Tag-AP2XII-1-IAA-2

value: T. gondii

value: RH

value: IAA treated


title: RNASEQ_SASD_biorep_3

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w APP ex 17 SA and SD Targeting gRNAs


title: SRSF5 iCLIP2 Replicate 3

value: HeLa

value: HeLa hGRAD SRSF5-GFP-endo

value: anti-GFP antibody

value: NNNNNTACAAGNNNN


title: RNASEQ_SASD_biorep_2


title: Cut-Tag-AP2XII-1-IAA-1


title: Cut-Tag-AP2XII-1-CTL-1

value: untreated


title: RNASEQ_SASD_biorep_1


title: SRSF5 iCLIP2 Replicate 2

value: NNNNNGCTCATNNNN

value: SRSF5-bound RNA


title: Multiplexed pool 3B, Feature barcode (antibody panel and hashtags)

first: Bridget

middle: P

last: Keenan

address: 505 PARNASSUS AVE, ROOM 1296

department: Medicine

institute: University of California San Francisco

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and VDJ barcode counts) was performed using the 10x Genomics Cell Ranger pipeline where ADT and GEX libraries were run together with one output file from cellranger.
For demultiplexing for PBMC scRNAseq data, we used the hashtag method using a threshold method for determining the identify of each single cell and removing doublets. Demultiplexed identities of each cell barcode are available in the cell_barcodes.csv supplemental file.
We used the scanpy data analysis pipeline for pre-processing and analysis of scRNAseq data, with the following software versions: Python 3.7.12, scanpy 1.9.1, anndata 0.8.0, leidenalg 0.8.10, scvi 0.16.0, scipy 1.7.3, numpy 1.21.6, pandas 1.3.5, statsmodels 0.13.2. We applied the following cutoffs for filtering high quality cells: <10% mitochondrial genes, >400 genes expressed per cell, and excluded platelets and red blood cells. We filtered out ribosomal and mitochondrial genes and genes detected in less than 20 cells. We then used scanpy to normalize, logarithmize, and scale the data, identify highly variable genes, and perform principal component analysis. We used scVI for batch correction prior to k-nearest neighbor graph construction and clustering on gene expression data with a resolution of 1.0 using the leiden algorithm. For proteins in the CITEseq dataset, we normalized and logarithmized the data.
Assembly: GRCh38 3.0.0
Supplementary files format and content: raw files: fastq; 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; VDJ cellranger output: comma separated values files
Library strategy: CITE-seq

molecule: protein

source_name: Peripheral blood

extract_protocol:
Blood samples were processed using ficoll (Cytiva); after centrifugation, the PBMC layer was isolated and cryopreserved in cell media with human serum and DMSO. Previously frozen PBMCs were thawed using media containing RPMI, heat-inactivated sterile filtered human serum, penicillin-streptomycin, non-essential amino acids, sodium pyruvate, and L-glutamine (CHM media). Samples were then incubated for DNAse I (15 units/mL, Roche).
After washing and counting, PBMCs were incubated in staining buffer (1 mM EDTA and 2% heat inactivated FBS in Dulbecco's phosphate-buffered saline (Thermo Fisher)) with TruStain FcX (Fc Receptor Blocking Solution, Biolegend) and Total-Seq C anti-human Hashtag antibodies (Biolegend) for a final hashtag dilution of 2000x. 1 x10>6 cells from 9 unique samples were combined and stained with one pooled cocktail containing a custom panel of 197 antibody-oligonucleotide conjugates targeting cell surface proteins of interest (see reference_antibodies.csv supplemental file, Biolegend) per manufacturer protocols.
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x 5ʹ Reagent Kits version 1, according to manufacturer instructions. 10X 5’ kits for feature barcoding and TCR and BCR amplification were used to generate libraries per manufacturer instructions.

value: Peripheral blood

value: Peripheral blood mononuclear cells

tag: library type

value: ADT

tag: antibodies/tags

value: see manuscript Table S3


title: Multiplexed pool 3A, B cell receptor

value: VDJ


title: Multiplexed pool 3B, B cell receptor


title: SRSF5 iCLIP2 Replicate 1

value: NNNNNAAGCTANNNN


title: Multiplexed pool 3A, Feature barcode (antibody panel and hashtags)


title: RNAseq 5TGM1 bortezomib resistant engraftable replicate-3

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

data_processing:
Illumina bcl2fastq Conversion Software v2.20 was used for basecalling
Raw reads were adapter trimmed using Cutadapt version 4.2 setting minimum-length option to 18, error-rate 0.2 and overlap 5
Trimmed reads were mapped against the mouse (mm10) reference genome using the STAR spliced alignment algorithm version 2.7.7a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: tab delimited file of raw gene counts

organism: Mus musculus

source_name: Bone marrow

growth_protocol: All cell lines grown in IMDM media with 20% fetal bovine serum + penicillin-streptomycin + L-glutamine + sodium pyruvate + HEPES. 5TGM1.BRE cells cultured in 10nM bortezomib, with media changed twice weekly.

extract_protocol:
RNA was extracted from 1x10^7 cells using the Qiagen RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell lines were removed from drug at least 72h before RNA extraction

value: Bone marrow

value: Murine myeloma cell line arising from serial passage of spontaneous bone marrow cell myeloma developed in C57Bl/KaLwRij mice and then cultured in bortezomib until resistant


title: Multiplexed pool 3B, Gene expression

value: Gene expression


title: Multiplexed pool 3A, T cell receptor


title: Multiplexed pool 3A, Gene expression


title: Cut-Tag-AP2XI-2-IAA-1

value: T. gondii

value: RH

value: IAA treated


title: Multiplexed pool 3B, T cell receptor


title: 4C-seq 80% epiboly stage, atRA, meis2a downstream

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

data_processing:
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the danRer10 assembly using Bowtie software.  Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept. Reads located in fragments flanked by two restriction sites of the same enzyme, or in fragments smaller than 40 bp were filtered out Mapped reads were then converted to reads-per-first-enzyme-fragment-end units, and smoothed using a 30 DpnII fragments mean running window algorithm.
Data visualization: data were uploaded to UCSC Browser for visualization.
Assembly: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary files format and content: bedGraph, they contain smoothed data of 4Cseq of viewpoint that can be directly uploaded to UCSC for visualization.
Library strategy: 4C-seq

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were grown at 28°C in E3 medium until desired developmental stage

extract_protocol:
Embryos were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for 4C-seq preparation as previously described (Acemel et al. 2016). Briefly, chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Preparation of 4C-seq libraries was performed as described for in Acemel et al., 2016. Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

treatment_protocol: Embryos were treated or not with 0.1 µM atRA at 30% epiboly and collected at 80% epiboly

value: whole embryo

tag: developmental stage

value: 80% epiboly

value: wild-type

value: atRA

tag: viewpoint

value: meis2a downstream


title: Cut-Tag-AP2XI-2-IAA-2


title: RNAseq 5TGM1 bortezomib resistant engraftable replicate-1

value: Murine myeloma cell line arising from serial passage of spontaneous bone marrow cell myeloma developed in C57Bl/KaLwRij mice


title: Cut-Tag-AP2V-2-IAA-1


title: Cut-Tag-AP2V-2-IAA-2


title: Multiplexed pool 2B, T cell receptor

value: Peripheral blood

value: Peripheral blood mononuclear cells


title: RNA-AP2XII-1-CTL-3

value: untreated


title: Multiplexed pool 2B, Feature barcode (antibody panel and hashtags)

value: ADT

value: see manuscript Table S3


title: Multiplexed pool 2B, Gene expression


title: RNA-AP2XII-1-CTL-2


title: Multiplexed pool 2A, Feature barcode (antibody panel and hashtags)


title: 4C-seq 80% epiboly stage, atRA, meis2a promoter

value: meis2a promoter


title: RNA-AP2XII-1-IAA-3


title: RNA-AP2XII-1-CTL-1


title: Multiplexed pool 2A, T cell receptor

value: VDJ


title: RNAseq 5TGM1 bortezomib resistant engraftable replicate-2

value: Bone marrow

value: Murine myeloma cell line arising from serial passage of spontaneous bone marrow cell myeloma developed in C57Bl/KaLwRij mice and then cultured in bortezomib until resistant


title: Multiplexed pool 2A, Gene expression

value: Gene expression


title: 4C-seq 80% epiboly stage, atRA, hoxb10a promoter

value: hoxb10a promoter


title: Multiplexed pool 2A, B cell receptor


title: Multiplexed pool 1B, Feature barcode (antibody panel and hashtags)


title: 4C-seq 80% epiboly stage, atRA, hoxb1a promoter

value: whole embryo

value: hoxb1a promoter


title: 4C-seq 80% epiboly stage, control, meis2a downstream

value: 80% epiboly

value: wild-type

value: control


title: RNA-AP2XII-1-IAA-2

value: T. gondii

value: RH

value: IAA treated


title: RNA-AP2XII-1-IAA-1


title: Multiplexed pool 1B, T cell receptor

value: Peripheral blood

value: Peripheral blood mononuclear cells


title: Multiplexed pool 1B, Gene expression


title: Multiplexed pool 1B, B cell receptor


title: Multiplexed pool 2B, B cell receptor


title: 4C-seq 80% epiboly stage, control, hoxb10a promoter


title: Multiplexed pool 1A, Feature barcode (antibody panel and hashtags)

value: ADT

value: see manuscript Table S3


title: RNA-AP2XI-2-CTL-3

value: untreated


title: Multiplexed pool 1A, B cell receptor

value: VDJ


title: ctrl2-3

city: Chengdu

first: Xinyi

last: Kuang

address: No.34, Renmin South road

institute: West China Hospital of Stomatology

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp 0.19.5 with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 2.1.0 software. The mapped reads of each sample were assembled by StringTie 2.1.2 in a reference-based approach.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKMvalues for each Sample

source_name: bone marrow

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent Technologies) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >10ng) was used to construct sequencing library.
Transcriptome library was prepared following Clontech-SMART-SeqTM v4 UltraTM Low Input RNA Kit for sequencing using 10ng of total RNA. Then the synthesized cDNA was conducted into library according to Illumina’s library construction protocol. Finally, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer (2 × 150bp read length).

value: bone marrow

tag: strain

value: Lin- Sca1+ cKit+


title: 4C-seq 80% epiboly stage, control, meis2a promoter

value: meis2a promoter


title: ctrl2-1

tag: cell type


title: RNA-AP2XI-2-CTL-2


title: 4C-seq 80% epiboly stage, control, hoxb1a promoter

value: whole embryo


title: shPCID2 J-Lat 11.1 2 [RC4]

city: Rotterdam

first: Tokameh

last: Mahmoudi

address: Dr Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Quant-Seq FASTQ files obtained from Ion Proton sequencing were mapped on the UCSC hg19 reference genome using a two-phase mapping procedure. Firstly, the short reads were mapped using tophat2(Kim et al., 2013), with the following non-default settings: --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --no-novel-juncs, other settings at default. Additional transcript annotation data for the hg19 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html) were also provided to tophat2 for guidance. Next, the reads that remained unmapped were converted back to FASTQ files using bam2fastq from the BEDTools (Quinlan and Hall, 2010) suite and submitted to a second round of mapping using Bowtie2 (Langmead and Salzberg, 2012) against the hg19 genome with the --local and --very-sensitive-local switches turned on. All resulting BAM files were visualized in the UCSC Genome Browser using BEDTools and tools provided by the UCSC Genome Browser toolkit
The resulting Quant-Seq BAM files were analyzed with the Bioconductor package metaseqR(Moulos and Hatzis, 2015), which has built-in support for Quant-Seq data. Briefly, the raw BAM files, one for each sample, were summarized to a 3’ UTR read counts table from Ensembl longest (dominant) transcripts (version 90). The original 3’ UTR regions were extended 500 bp upstream and downstream to accommodate the variable read length of Ion Proton reads. In the resulting read counts table, each row represented one 3’ UTR region, each column one Quant-Seq sample, and each cell the corresponding read counts associated with each row and column. The final 3’ UTR read counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq (Anders et al., 2012) after removing areas that had zero counts over all the Quant-Seq samples. Prior to the statistical testing procedure, the 3’ UTR read counts were filtered for possible artifacts that could affect the subsequent statistical testing procedures. 3’ UTR areas presenting any of the following were excluded from further analysis: (i) 3’ UTR areas corresponding to genes smaller than 500 bp,(ii) 3’ UTRs with read counts below the median read counts of the total normalized count distribution (similar expression thresholds [e.g., the median of the count distribution] have been previously used in the literature[Mokry et al., 2012], where the authors use the median reads per kilobase of transcript, per million mapped reads(RPKM) value instead of normalized counts), and(iii) 3’ UTR areas corresponding to genes with the following Ensembl biotypes: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V pseudogene.
Differentially expressed gene analysis of obtained reads was performed using edgeR package under Galaxy (https://usegalaxy.eu/). Cut-off for false discovery rate was 0.01 and a 1.5 fold change for differentially expressed. Volcano plots were generated using Galaxy (https://usegalaxy.eu/)
Assembly: UCSC hg19
Supplementary files format and content: tab delimited text file includes normalized counts for each sample

source_name: Blood

extract_protocol:
Cells were lysed with TRI reagent (Sigma) and total cell-associated RNA was isolated following manufacturer instructions.
cDNA libraries were generated using the 3’ mRNA-seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN) following manufacturer’s instructions

value: Blood

value: Jurkat J-Lat 11.1

value: Lymphocyte


title: RNA-AP2XI-2-CTL-1


title: Multiplexed pool 1A, Gene expression

value: Gene expression


title: Multiplexed pool 1A, T cell receptor


title: RNA-AP2XI-2-IAA-3

value: T. gondii


title: uc1-3

value: DSS-induced colitis


title: shPCID2 J-Lat 11.1 1 [RC3]


title: RNA-AP2XI-2-IAA-2

value: RH

value: IAA treated


title: uc1-2


title: Patient_05, Surgical resection, B cell receptor

description: 10x Genomics

data_processing:
All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression and 5,000 reads for TCR/BCR/protein libraries.
CellRanger version 3.1.0 (10x Genomics, Genome Build: GRCh38 3.0.0) was used to align the raw sequencing data.
We used doubletdetection to identify doublet cells from the single cell data. We used the scanpy data analysis pipeline for pre-processing and analysis of scRNAseq data, with the following software versions: Python 3.7.12, scanpy 1.9.1, anndata 0.8.0, leidenalg 0.8.10, scvi 0.16.0, scipy 1.7.3, numpy 1.21.6, pandas 1.3.5, statsmodels 0.13.2. We applied the following cutoffs for filtering high quality cells: <10% mitochondrial genes, >400 genes expressed per cell, and excluded platelets and red blood cells. We filtered out ribosomal and mitochondrial genes and genes detected in less than 20 cells. We then used scanpy to normalize, logarithmize, and scale the data, identify highly variable genes, and perform principal component analysis. We used scVI for batch correction prior to k-nearest neighbor graph construction and clustering on gene expression data with a resolution of 1.0 using the leiden algorithm.
Assembly: GRCh38 3.0.0
Supplementary files format and content: raw files: fastq; 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; VDJ cellranger output: comma separated values files

extract_protocol:
Tumor tissue samples were digested in RPMI containing Collagenase I & II (0.1 mg/ml, Thermo Fisher Scientific) and DNAse I, minced, and digested for one hour using the GentleMACS system (Miltenyi Biotec). Isolation of live cells was performed using MACS LS columns (Miltenyi Biotec).
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x 5ʹ Reagent Kits version 1, according to manufacturer instructions. 10X 5’ kits for TCR and BCR amplification were used to generate libraries per manufacturer instructions.

value: Immune and tumor cells

tag: timepoint

value: surgical resection


title: shControl J-Lat 11.1 2 [RC2]

value: shControl


title: RNA-AP2XI-2-IAA-1


title: Patient_05, Surgical resection, T cell receptor

description: 10x Genomics


title: ctrl2-2

value: control


title: uc1-1


title: shControl J-Lat 11.1 1 [RC1]


title: NMUKO_EXO

source_name: NMuMG

value: NMuMG

value: mammary epithelial cells

value: CREPT knockout

value: CDEs-treated


title: RNA-AP2V-2-CTL-3

value: untreated


title: Patient_05, Surgical resection, Gene expression

description: 10x Genomics


title: Patient_05, Post-sotigalimab, B cell receptor

description: 10x Genomics

value: post-sotigalimab

value: VDJ


title: RNA-AP2V-2-CTL-2


title: RNA-AP2V-2-CTL-1


title: lung endothelial cells (CD45- EPCAM-CD31+) from day D30 post-influenza

city: Philadelphia

first: Gan

last: Zhao

state: PA Pennsylvania

address: 384E Old Vet Quad 3800 spruce street

institute: University of Pennsylvania

description: mouse lung endothelial cells 30 days post-influenza

data_processing:
Cellranger 3.1.0
Cellranger mkfastq
Assembly: GRCm38 - mm10
Supplementary files format and content: h5 files from the ouput of cellranger, containing matrix, barcodes, and features

source_name: mouse lung 30 days post-influenza

extract_protocol:
cells sorted straight into PBS + 0.1% BSA and loaded on 10x Chromium device
Chromium Single Cell 3ʹ Feature Barcode Library Kit

value: post-influenza endothelial cells sorted from  day 30 post-influenza mouse lungs

value: lung endothelial single cell


title: lung endothelial cells (CD45- EPCAM-CD31+) from day D20 post-influenza

description: mouse lung endothelial cells 20 days post-influenza

source_name: mouse lung 20 days post-influenza

value: post-influenza endothelial cells sorted from  day 20 post-influenza mouse lungs


title: NMUKO

value: PBS-treated


title: Patient_05, Post-sotigalimab, T cell receptor

description: 10x Genomics


title: NMUWT_EXO

value: WT


title: lung endothelial cells (CD45- EPCAM-CD31+) from day D0 post-influenza(Uninjured)

description: mouse lung endothelial cells 0 days post-influenza

source_name: mouse lung 0 days post-influenza

value: post-influenza endothelial cells sorted from  day 0 post-influenza mouse lungs


title: RNA-AP2V-2-IAA-3

value: T. gondii

value: RH

value: IAA treated


title: Patient_05, Post-sotigalimab, Gene expression

description: 10x Genomics

value: Immune and tumor cells

value: Gene expression


title: AP (96 hours), scRNAseq

city: Fuzhou

first: Changgan

last: Chen

state: --- Select One ---

address: #29 Xinquan Road, Fuzhou 350001, People’s Republic of China

institute: Fujian Medical University Union Hospital

description: 10x Genomics

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with Cellranger count module to generate feature-barcode matrix and determine clusters. The Seurat pipeline was applied to the data.
Genes expressed in less than three cells and cell expressed less than 400 and more than 5,000 genes were excluded. The data were normalized. Most variable genes were detected by the FindVariableFeatures function and used for subsequent analysis.
Principle component analysis (PCA) was performed on about 3000 genes with PCA function. The first 40 PCA components were used for the tSNE dimension reduction of the scaling matrix (with only the majority of variable genes) to obtain a two-dimensional representation of the cell state.
For clustering, we used FindClusters function, which realized the modular and optimized clustering algorithm of SNN (Shared nearest neighbor) based on 40 PCA components. The clusters were annotated to known biological cell types according to the expression of canonical markers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Peripheral blood from control (0 hours), initial phase of AP (12 hours and 24 hours) and recovery phases (96 hours) were collected. The PBMCs were isolated from peripheral blood by Ficoll-Hypaque gradient centrifugation (Haoyang Biotech, Tianjin, China).
Single-cell RNA sequencing was performed on single-cell suspensions from peripheral blood with viability > 90%. Using single cell 5 'Library and Gel Bead Kit (10xGenomics, 1000006) and Chromium Single Cell A Chip Kit (10x Genomics, 120236), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Single-cell RNA-seq libraries were constructed using Single Cell 5’ Library and Gel Bead Kit. The libraries were sequenced using an Illumina Novaseq6000 sequencer.

value: PBMCs

value: Blood

value: C57BL/6J, wild type

tag: age

value: 6-8 weeks old


title: RNA-AP2V-2-IAA-2


title: Normal1

data_processing:
Fastq files were analyzed with spaceranger version 1.3.1
Assembly: GRCh38 (Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv)
Supplementary files format and content: aligned_fiducials.jpg: aligned image fiducials
Supplementary files format and content: barcodes.tsv.gz: spatial barcodes list
Supplementary files format and content: detected_tissue_image.jpg: image of tissue with spots
Supplementary files format and content: features.tsv.gz: list of genes
Supplementary files format and content: matrix.mtx.gz: gene expression counts
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution tissue image
Supplementary files format and content: tissue_lowres_image.png: low resolution tissue image
Supplementary files format and content: tissue_positions_list.csv: spatial barcodes and spot coordinates
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Normal control skin

extract_protocol:
Formalin fixed, paraffin embedded skin was sectioned and captured with the Visium Spatial Gene Expression kit.
Gene expression libraries were prepared following the 10x Genomics Visium Spatial Gene Expression protocol.
Probe based amplification of mRNA

value: Normal control skin


title: Patient_05, Pre-sotigalimab, T cell receptor

description: 10x Genomics

value: pre-treatment

value: VDJ


title: HS2

source_name: HS lesional skin

value: HS lesional skin


title: RNA-AP2V-2-IAA-1


title: Patient_05, Pre-sotigalimab, Gene expression

description: 10x Genomics


title: AP (24 hours), scRNAseq

description: 10x Genomics


title: HS1


title: AP (12 hours), scRNAseq

description: 10x Genomics


title: Patient_04, Surgical resection, B cell receptor

description: 10x Genomics

value: surgical resection


title: Control (0h), scRNAseq

description: 10x Genomics


title: Patient_04, Surgical resection, Gene expression

description: 10x Genomics


title: Patient_04, Post-sotigalimab, T cell receptor

description: 10x Genomics

value: post-sotigalimab


title: NMUWT

value: NMuMG

value: mammary epithelial cells

value: WT

value: PBS-treated


title: L_2M_p21G3TKO_2

city: Kunming

first: Juhua

last: Dan

state: Yunnan

address: 727 South of Jingming Road

department: Medical School

institute: Kunming University of Science and Technology

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Liver

growth_protocol: normal feed

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: different genotype

value: Liver


title: neonatal femur bone, cartilage, and stromal progenitors

city: Stanford

first: Malachia

last: Hoover

address: 265 Campus Drive Room G3105

institute: Stanford University

description: gene expression data from neonatal femur BCSPs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Genechip Scanner 3000 (Affymetrix)

data_processing: Data generated was then exported to DCHIP software for normalization. The raw microarray dataset was uploaded to the Gene Expression Commons platform (https://gexc.stanford.edu/). Here, normalization against the Common Reference, a vast dataset (n = 11,939) from the National Center for Biotechnology Information Gene Expression Omnibus, was carried out. An in-depth meta-analysis of the Common Reference was performed to establish the dynamic range of each gene's probe set. For analysis, the probe set exhibiting the broadest dynamic range was chosen.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: neonatal mice were collected three days after birth

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The designated region-of-interest (ROI) was carefully dissected, and cells were subsequently isolated through a combined approach involving mechanical separation and collagenase digestion. Following this, the solution underwent centrifugation, post which the supernatant was carefully discarded. The residual cell pellet was then resuspended in a FACS buffer solution. These cells were then subjected to staining using antibodies targeted against specific antigens: CD45, Ter119, CD202b, Thy1.1, Thy1.2, CD105, CD51, 6C3, and a streptavidin-conjugated antibody for CD200. To identify and exclude any non-viable cells, propidium iodide was employed. The FACS analysis was executed on an FACS Aria II Instrument (BD Biosciences)

value: neonatal femur

tag: tissue region

value: femur

value: BCSP

value: C57BL/6J mice

value: postnatal day 3


title: Patient_05, Pre-sotigalimab, B cell receptor

description: 10x Genomics

value: Immune and tumor cells


title: neonatal femur skeletal stem cells

description: gene expression data from neonatal femur SSCs

source_name: neonatal femur skeletal stem cells

value: SSC


title: neonatal lumbar bone, cartilage, and stromal progenitors

description: gene expression data from neonatal lumbar BCSPs

value: neonatal spine

value: lumbar


title: L_2M_p21G3TKO_1


title: L_2M_G3DKO_3


title: cebpb_mut_KM_2

city: Guangzhou

first: Gaofei

last: Li

address: Guangzhou Higher Education Mega Centre, Panyu District

institute: South China University of Technology

data_processing:
Post basecalling, the fastq files were mapped to the zebrafish genome with the CellRanger package.
Output files of CellRanger were applied to the R package "Seurat".
Samples were filtered to remove low quality or contaminated cells.
The renal cells from different genotypes (sample 1-9) were integrated with the "IntegrateData" function of Seurat.
Further analyses was performed based on the instructions of "Seurat" package.
Assembly: GRCz11
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell, cell and gene metadata for integrated KM cells and KM eosinophils, and the relevant Seurat objects (rds files).

source_name: renal cells

extract_protocol:
For scRNA-Seq analysis of eosinophils from kidney, eosinophils were sorted from adult Tg(eslec:eGFP) kidneys. For scRNA-Seq analysis of renal cells of different genotypes, kidneys were collected from WT, cebp1-/-, and cebpb-/- individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x 3' scRNA-Seq GEM generation.
Post GEM generation, the library construction was performed strictly based on the manufacturer’s instructions (10x Genomics, USA).

value: AB strain

value: Kidney

value: cebpb-/-

tag: transgene


title: cebpb_mut_KM_3


title: cebpb_mut_KM_1


title: cebp1_mut_KM_2


title: Patient_04, Post-sotigalimab, Gene expression

description: 10x Genomics

value: post-sotigalimab

value: Gene expression


title: neonatal thoracic bone, cartilage, and stromal progenitors

description: gene expression data from neonatal thoracic BCSPs

value: thoracic


title: KM_eos

source_name: eosinophils

value: wild type


title: L_2M_G3DKO_2

value: Liver


title: Patient_03, Post-sotigalimab, Gene expression

description: 10x Genomics


title: WT_KM_3


title: cebp1_mut_KM_1


title: Patient_04, Post-sotigalimab, B cell receptor

description: 10x Genomics

value: VDJ


title: neonatal cervical bone, cartilage, and stromal progenitors

description: gene expression data from neonatal cervical BCSPs

value: cervical


title: cebp1_mut_KM_3


title: Patient_03, Pre-sotigalimab, T cell receptor

description: 10x Genomics

value: pre-treatment


title: WT_KM_2


title: Patient_03, Pre-sotigalimab, Gene expression

description: 10x Genomics


title: SASD_mouse_bulk_RNA_biorep_3

description:
23M3_bulk_ RNA
Hipocampus extraction; RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

data_processing:
Crispresso2 utilized for base calling and base editing frequency quantification for all DNA NGS files. Sequences were filtered for 90% homology with a phred33 read qualitty of >30. Sequencecs were aligned to an inputted PCR amplicon with the gRNA region of interest
RNAstar utilized for exon junction analysis, creating bam and SJ outputs to visualize and quantify RNA splicing. 2-pass mapping was used with a MAPQ quality score of 60
Assembly: chr38
Supplementary files format and content: Excel sheet containing editing data sorted by figure number; .txt file containing nucleotide frequencies
Supplementary files format and content: DNA base editing analysis outputted in .txt files containing nucleotide frequencies in gRNA windows
Supplementary files format and content: RNAstar files outputted as .txt files containing splice junctions and quantification of junction occurance

source_name: hippocampus

extract_protocol:
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits and utilized manufacturer protocols
Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: hippocampus

value: neuron

value: 650kb YAC insert human APP(K670N/M671L), copy number ~3

tag: treatment

value: AAVrh10 split SpRY-ABE8e APP ex17 SA and SD Targeting gRNAs

tag: Sex

value: male


title: neonatal cervical skeletal stem cells

description: gene expression data from neonatal cervical SSCs

source_name: neonatal cervical skeletal stem cells

value: neonatal spine

value: SSC

value: C57BL/6J mice

value: postnatal day 3


title: WT_KM_1

value: AB strain

value: Kidney

tag: genotype


title: neonatal thoracic skeletal stem cells

description: gene expression data from neonatal thoracic SSCs

source_name: neonatal thoracic skeletal stem cells

value: thoracic


title: Hyperoxia 5

first: Xuewen

address: 1650 Owens Street

institute: Gladstone Institutes

description:
R_S62_L002_R1_001
3' mRNA-seq (Quant-seq)

data_processing:
The genes were aligned and the expressions were quantified using the kallisto pseudoaligner (v 0.46.1)
The data were normalized using the count per million (CPM) method.
The statistics analysis was performed using limma (v 3.54.2)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes log count per million (CPM) for each sample

source_name: Lung

growth_protocol: C57BL/6J (IMSR_JAX: 000664) male mice (7-week-old) were purchased from Jackson Laboratory. Upon delivery, the mice were housed in the UCSF animal facility. Different oxygen levels (8, 60 or 80% O2) were created by mixing N2 (Airgas), O2 (Airgas, Praxair), and room air carefully controlled by gas regulators.

extract_protocol:
Tissues were homogenized in TRIzol Reagent (ThermoFisher 15596026) using the Qiagen Tissue Lyser II (30 Hz, 2 min). RNA extraction was performed according to the manufacturer’s instructions. RNA purity and integrity were determined using NanoDrop One (ThermoFisher) and Bioanalyzer (Agilent), respectively.
The Quant-seq library preparation was carried out using the Lexogen QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (#191.96). Equal amounts of RNA (500 ng) from samples (n = 7 for nomorxia, and n = 6 for hyperoxia) were used for the preparation, according to the manufacturer’s guide. Following the PCR amplification, the cDNA concentrations were examined using a Qubit™ dsDNA HS and BR Assay Kit (Invitrogen Q32851) on a Qubit 4 Fluorometer (ThermoFisher). The average library sizes were determined using TapeStation 4200 (Agilent). Next, equal amounts of cDNA with Unique Dual Indices (UDIs) were pooled and sequenced on an Illumina’s NovaSeq 6000 System in the UCSF Center for Advanced Technology (CAT).

treatment_protocol: Mice were exposed to 21% or 80% oxygen for 5 days. Mouse lung tissues were perfused with cold DPBS, and flash frozen in liquid nitrogen.

value: Lung

value: WT

value: Hyperoxia (80percent)


title: neonatal lumbar skeletal stem cells

description: gene expression data from neonatal lumbar SSCs

source_name: neonatal lumbar skeletal stem cells

value: lumbar


title: Hyperoxia 6

description:
S_S63_L002_R1_001
3' mRNA-seq (Quant-seq)


title: SASD_mouse_bulk_DNA_biorep_3

description:
23M3_bulk_ DNA
Hipocampus extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency

tag: cell line


title: Patient_03, Post-sotigalimab, T cell receptor

description: 10x Genomics

value: Immune and tumor cells

value: post-sotigalimab

value: VDJ


title: Patient_02, Post-sotigalimab, B cell receptor

description: 10x Genomics


title: Hyperoxia 4

description:
Q_S61_L002_R1_001
3' mRNA-seq (Quant-seq)


title: L_2M_p21G3TKO_3

value: Liver


title: ROSA_GFP_sorted_DNA_biorep_3

description:
23M1_GFP_ DNA
Hipocampus; nucleus extraction; GFP+ Nuclei enrichment; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: hippocampus

value: neuron

value: 650kb YAC insert human APP(K670N/M671L), copy number ~3

value: AAVrh10 split SpRY-ABE8e ROSA Targeting gRNA


title: cebpb_wt_eos_2

data_processing:
Post quality-control, the fastq files were mapped to the zebrafish genome with the "STAR" package.
Mapped reads were annotated with the "FeatureCounts" package.
Annotated reads were applied to the "DESeq2" package for differential expressed genes analysis.
The sample-to-sample distance heatmaps were generated by "pheatmap" with the output of "DESeq2".
The gene expression heatmaps were generated by "pheatmap" with the Z-score of the TPM matrix.
Assembly: GRCz11
Supplementary files format and content: Normalized matrix table with Transcripts Per Kilobase (TPM) for every gene and every sample

extract_protocol:
Whole larvae were ground and digested into cell suspensions. The cell suspensions were then analyzed with FACS and the eGFP+ cells  (~500 cells for each sample) were sorted into lysis buffer.
The lysates were directly applied to reverse transcription and amplification. Enriched cDNA were then fragmented, adpator tagged, and purified for further sequencing.

value: whole larvae

value: wild type


title: ROSA_bulk_RNA_biorep_3

description:
23M1_bulk_ RNA
Hipocampus extraction; RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: male


title: Normoxia 7

description:
P_S60_L002_R1_001
3' mRNA-seq (Quant-seq)

value: Normoxia (21percent)


title: Patient_02, Post-sotigalimab, Gene expression

description: 10x Genomics

value: Gene expression


title: cebpb_mut_eos_2

value: AB strain

value: cebpb-/-


title: Normoxia 6

description:
O_S59_L002_R1_001
3' mRNA-seq (Quant-seq)

value: Lung

value: WT


title: L_2M_G3DKO_1


title: ROSA_mouse_bulk_DNA_biorep_3

description:
23M1_bulk_ DNA
Hipocampus extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency


title: cebpb_mut_eos_1


title: Patient_01, Pre-sotigalimab, B cell receptor

description: 10x Genomics

value: Immune and tumor cells

value: pre-treatment


title: Patient_01, Pre-sotigalimab, T cell receptor

description: 10x Genomics

value: VDJ


title: cebp1_wt_eos_2


title: Hyperoxia 3

description:
M_S58_L002_R1_001
3' mRNA-seq (Quant-seq)

value: Hyperoxia (80percent)


title: ROSA_mouse_GFP_sorted_DNA_biorep_2

description:
22M5_GFP_ DNA
Hipocampus; nucleus extraction; GFP+ Nuclei enrichment; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: hippocampus


title: cebp1_wt_eos_1


title: Hyperoxia 2

description:
L_S57_L002_R1_001
3' mRNA-seq (Quant-seq)


title: Patient_02, Post-sotigalimab, T cell receptor

description: 10x Genomics

value: post-sotigalimab


title: Patient_01, Pre-sotigalimab, Gene expression

description: 10x Genomics


title: Hyperoxia 1

description:
J_S56_L002_R1_001
3' mRNA-seq (Quant-seq)


title: cebpb_wt_eos_1


title: ROSA_mouse_bulk_DNA_biorep_2

description:
22M5_bulk_ DNA
Hipocampus extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency

value: neuron

value: 650kb YAC insert human APP(K670N/M671L), copy number ~3


title: cebp1_mut_eos_2

value: whole larvae


title: Nascent-seq SRSF5 depletion T16 Replicate 2

description: RNA-seq

data_processing:
RNA-seq: Reads were mapped to the human genome hg38 using STAR (v2.6.1d) with default parameters. Mapped reads were counted with htSeq-count.
Mapped reads were analysed with DESeq2 for differential expression and IRFinder for intron retention.
Assembly: GRCh38.p12 (Gencode release 31)
Supplementary files format and content: Count tables in .txt format.

source_name: HeLa

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and 1% penicilin at 37˚C with 5% CO2.

extract_protocol:
The reaction was stopped by applying TRIzol™RI reagent to the culture dishes. RNA extraction and pulldown of newly transcribed RNA was performed according to (Gressel et al., 2019, PMID: 31399571) without fractionation of the RNA by sonification. Nascent RNA was purified using RNA Clean and Concentrate Kit (ZymoResearch).
cDNA libraries for RNA-seq were prepared with universal Plus™ Total RNA-Seq Library Preparation Kit (Tecan) according to manufacturer's instructions. Ribosomal RNA fragments were removed and the library was sequenced on an Illumina NovaSeq6000 instrument
strand-specific

treatment_protocol: Cells were treated with 1µg/ml Doxycyclin to start SRSF5 protein degradation. SRSF5 depletion was allowed for 2h, 8h and 16h. One hour before harvesting, cells were incubated with 400 µM 4-sU for exactly 1 hour to label newly transcribed RNAs.

value: HeLa

value: HeLa hGRAD SRSF5-GFP-endo

tag: time

value: nascent RNA


title: SASD_mouse_GFP_sorted_DNA_biorep_3

description:
22M4_GFP_ DNA
Hipocampus; nucleus extraction; GFP+ Nuclei enrichment; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: AAVrh10 split SpRY-ABE8e APP ex17 SA and SD Targeting gRNAs

value: male


title: Normoxia 4

description:
F_S54_L002_R1_001
3' mRNA-seq (Quant-seq)

value: Normoxia (21percent)


title: cebp1_mut_eos_1

value: AB strain


title: SASD_mouse_bulk_RNA_biorep_2

description:
22M4_bulk_ RNA
Hipocampus extraction; RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: Nascent-seq SRSF5 depletion T16 Replicate 1

description: RNA-seq

tag: fraction


title: Nascent-seq SRSF5 depletion T8 Replicate 2

description: RNA-seq


title: Nascent-seq SRSF5 depletion T8 Replicate 1

description: RNA-seq


title: SASD_mouse_GFP_sorted_DNA_biorep_2

description:
20M4_GFP_ DNA
Hipocampus; nucleus extraction; GFP+ Nuclei enrichment; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

tag: tissue


title: cebpb_input_2

data_processing:
Post quality-control, the fastq files were mapped to the zebrafish genome with the "BWA-MEM" package.
Aligned reads were then filtered by "Samtools", with peak-calling by "MACS2".
Peaks were annotated with "ChIPseeker" to identify Cebp1- and Cebpβ-binding genes.
The aligned reads were converted from BAM formats into Bigwig formats by "deepTools".
Bigwig files were visualized with the Integrative Genomics Viewer.
Assembly: GRCz11
Supplementary files format and content: Bigwig files showing the enriched DNA regions for each sample

source_name: whole larvae

extract_protocol:
At 5 dpf, ~200 larvae for each sample were lysed, crosslinked, sonicated, antibody-incubated, de-crosslinked, and purified. Input samples were collected directly from sonication products as controls.
Library construction was prepared with purified DNA using NEBnext Ultra II based on the manufactors' instrutions.

treatment_protocol: We used Tg(hsp70:cebp1-eGFP) and Tg(hsp70:cebpb-eGFP) larvae to enrich Cebp1-eGFP or Cebpβ-eGFP fusion proteins by activating the hsp70 promoter at 39 °C. Larvae were heat-shocked for 2 hours/day from 2–5 dpf.

value: wild type


title: cebpb_input_1


title: Normoxia 3

description:
E_S53_L002_R1_001
3' mRNA-seq (Quant-seq)

value: Lung

value: WT


title: cebpb_ChIP_2


title: Normoxia 2

description:
C_S52_L002_R1_001
3' mRNA-seq (Quant-seq)


title: SASD_mouse_bulk_DNA_biorep_2

description:
20M4_bulk_ DNA
Hipocampus extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency


title: Nascent-seq SRSF5 depletion T2 Replicate 2

description: RNA-seq


title: Normoxia 1

description:
B_S51_L002_R1_001
3' mRNA-seq (Quant-seq)


title: ROSA_bulk_RNA_biorep_2

description:
22M5_bulk_ RNA
Hipocampus extraction; RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: AAVrh10 split SpRY-ABE8e ROSA Targeting gRNA


title: Total RNA of Mtb cells in the log phase Rep -2

city: Newyork

first: Xiangwu

last: Ju

address: 1230 York Avenue

institute: The Rockefeller University

description: Total RNA

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to Mtb(NC_018143.2 ) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Mycobacterium tuberculosis H37RV, NC_018143.2
wig files

organism: Mycobacterium tuberculosis

source_name: whole cell

growth_protocol: Mycobacterium tuberculosis (Mtb) H37Rv was grown at 37 °C in a minimal medium (Difco Middlebrook 7H9 broth) supplemented with 0.5% (v/v) glycerol, 0.05% (v/v) tyloxapol, 0.2 g L-1 casamino acids, 0.024 g L-1 pantothenic acid and 10% (v/v) OADC (BD). The double auxotrophic Mtb mc2 6206 strain (H37Rv ΔpanCD ΔleuCD)21 was grown in minimal medium with an additional 50 mg L-1 L-leucine (Sigma) and 24 mg mL-1  pantothenic acid (Sigma).

extract_protocol:
Bacterial cells were quenched by adding 1x vol of GTC buffer (600 g L-1 guanidium thiocyanate, 5 g L-1 N-laurylsarcosine and 7.1 g L-1 sodium citrate and 0.7% (v/v) 2-mercaptoethanol) to the culture medium immediately before the harvest and placed it at room temperature for 15 min. Cell pellets were collected by centrifugation (4,000 g for 10 min at 4 °C), then thoroughly resuspended in 100 μl of TE buffer (10 mM Tris-HCl and 1 mM EDTA, pH8.0). After adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and 300 mg of glass beads (Sigma,  G1145), the cells were immediately lysed by bead beating with the Precellys Evolution homogenizer at the highest speed 10,000 rpm for 4x 45s cycles with interval of 60s at 4°C. Then the RNA was extracted following TRIzol RNA purification protocol.
SEnd-seq strategy was used to prepare the SEnd-seq library

treatment_protocol: RNA  samples were collected when Mtb cells reached to log phase or stationary phase, or Mtb cells upon treatments of indicated antibiotics at different time points.

value: whole cell

value: bacteria

value: log phase growth


title: SASD_mouse_bulk_RNA_biorep_1

description:
20M2_bulk_ RNA
Hipocampus extraction; RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: hippocampus

value: neuron


title: Nascent-seq SRSF5 depletion T2 Replicate 1

description: RNA-seq


title: Normoxia 5

description:
G_S55_L002_R1_001
3' mRNA-seq (Quant-seq)


title: SASD_mouse_GFP_sorted_DNA_biorep_1

description:
20M2_GFP_ DNA
Hipocampus; nucleus extraction; GFP+ Nuclei enrichment; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: 650kb YAC insert human APP(K670N/M671L), copy number ~3


title: SASD_mouse_bulk_DNA_biorep_1

description:
20M2_bulk_ DNA
Hipocampus extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency


title: cebpb_ChIP_1

value: whole larvae


title: Nascent-seq SRSF5 depletion T0 Replicate 2

description: RNA-seq

value: HeLa

value: HeLa hGRAD SRSF5-GFP-endo


title: Nascent-seq SRSF5 depletion T0 Replicate 1

description: RNA-seq

value: nascent RNA


title: ROSA_mouse_bulk_RNA_biorep_1

description:
20M1_bulk_ RNA
Hipocampus extraction; RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: male


title: cebp1_input_1


title: cebp1_input_2


title: primary RNA of Mtb cells in the log phase Rep -3

description: primary RNA (5'PPP RNA)


title: cebp1_ChIP_2


title: VMRC-LCD cells, OE of ZFP36L1

city: Bunkyo-ku

first: Takayoshi

last: Enokido

state: Tokyo

address: 7-3-1 Hongo

department: Respiratory Medicine

country: Japan

institute: The University of Tokyo

description: VZ

data_processing:
CLC Genomics Workbench v 21.0.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: VMRC-LCD

extract_protocol:
RNA was harvested using FastGene RNA Premium Kit (Nippon Genetics, Tokyo). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA Library Prep. Kit following manufacturer's protocols.

value: VMRC-LCD

value: lung cancer cells

value: ZFP36L1 overexpression


title: primary RNA of Mtb cells in the log phase Rep -2

description: primary RNA (5'PPP RNA)


title: VMRC-LCD cells, OE of Control

description: VN


title: ROSA_mouse_GFP_sorted_DNA_biorep_1

description:
20F2_GFP_ DNA
Hipocampus; nucleus extraction; GFP+ Nuclei enrichment; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: female


title: ROSA_mouse_bulk_DNA_biorep_1

description:
20F2_bulk_ DNA
Hipocampus extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency


title: primary RNA of Mtb cells in the log phase Rep -1

description: primary RNA (5'PPP RNA)

value: WT


title: Total RNA of Mtb cells in the log phase Rep -1

description: Total RNA


title: cebp1_ChIP_1

value: AB strain

value: wild type


title: TS15-88_tECM

status: Public on Dec 09 2023

city: Seoul

first: Junseong

last: Park

address: 222 Banpo-daero, Seocho-gu

department: Cancer Evolution Research Center

country: South Korea

institute: The Catholic University of Korea

description:
TS15-88_tECM
SAMPLE 45

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were variance stabilizing transformed and quantile normalized using the R/Bioconductor lumi package.

label: Biotin

source_name: Glioblastoma tumorsphere

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

growth_protocol: Glioblastoma tumorspheres were cultured on different culture platforms: (1) collagen-based 3D matrix, (2) patient normal ECM (nECM)-based 3D matrix, (3) patient tumor ECM (tECM)-based 3D matrix, and (4) mouse brain.

extract_protocol: Total RNA was extracted from the tumor mass using a Qiagen RNeasy Plus Mini kit.

value: Brain

value: Male

tag: tumorsphere

tag: culture platform

value: tECM


title: TS15-88_mouse_1

description:
TS15-88_mouse
SAMPLE 46

value: mouse xenograft


title: TS14-15_nECM_3

description:
TS14-15_nECM
SAMPLE 37

value: nECM


title: TS14-15_Collagen_1

description:
TS14-15_Collagen
SAMPLE 32

value: Collagen


title: TS14-15_Collagen_3

description:
TS14-15_Collagen
SAMPLE 34


title: TS14-15_mouse_1

description:
TS14-15_mouse
SAMPLE 41


title: TS14-15_nECM_1

description:
TS14-15_nECM
SAMPLE 35


title: TS14-08_mouse_1

description:
TS14-08_mouse
SAMPLE 30

value: Female


title: TS14-15_Collagen_2

description:
TS14-15_Collagen
SAMPLE 33


title: TS15-88_mouse_2

description:
TS15-88_mouse
SAMPLE 47


title: TS14-15_tECM_1

description:
TS14-15_tECM
SAMPLE 38


title: TS14-08_tECM_3

description:
TS14-08_tECM
SAMPLE 29


title: TS15-88_nECM

description:
TS15-88_nECM
SAMPLE 44


title: TS14-08_nECM_1

description:
TS14-08_nECM
SAMPLE 25


title: TS14-08_tECM_1

description:
TS14-08_tECM
SAMPLE 27


title: TS14-15_tECM_3

description:
TS14-15_tECM
SAMPLE 40


title: TS14-15_mouse_2

description:
TS14-15_mouse
SAMPLE 42


title: TS14-08_nECM_2

description:
TS14-08_nECM
SAMPLE 26


title: TS14-15_tECM_2

description:
TS14-15_tECM
SAMPLE 39


title: TS15-88_Collagen

description:
TS15-88_Collagen
SAMPLE 43


title: TS14-15_nECM_2

description:
TS14-15_nECM
SAMPLE 36


title: TS13-64_tECM

description:
TS13-64_tECM
SAMPLE 21


title: TS13-64_mouse_1

description:
TS13-64_mouse
SAMPLE 22


title: TS13-64_Collagen

description:
TS13-64_Collagen
SAMPLE 19


title: TS13-64_nECM

description:
TS13-64_nECM
SAMPLE 20


title: TS14-08_mouse_2

description:
TS14-08_mouse
SAMPLE 31


title: TS14-08_tECM_2

description:
TS14-08_tECM
SAMPLE 28


title: TS13-64_mouse_2

description:
TS13-64_mouse
SAMPLE 23


title: TS13-20_tECM4_3

description:
TS13-20_tECM
SAMPLE 17


title: TS13-20_mouse

description:
TS13-20_mouse
SAMPLE 18


title: ESR1-YAP1_shESR1_Veh3

city: Pittsburgh

first: Megan

middle: E.

last: Yates

state: PA

address: 5051 Centre Ave

institute: University of Pittsburgh

data_processing:
RStudio Version 4.0.0
Transcript counts were quantified using Salmon v1.3.0 with parameters --seqBias --gcBias -p 8 -o and index hg38.
Gene-level counts were generated using tximport (Soneson et al., 2015) version 1.18.0.
Differential gene expression analysis was performed using the DESeq2 package version 1.30.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files including tximport abundance, count and lengths for each gene in each sample.

source_name: T47D shESR1

growth_protocol: Cells were grown in RPMI-1640 (#11875-119, Life Technologies) media at 37 °C and 5% CO2 before three days of hormone deprivation (media change to improved MEM (#MT10026CV, Fisher Scientific) supplemented with 10% CSS). Cells were seeded into 6 well plates and allowed to adhere overnight before the 24-hour treatment.

extract_protocol:
RNA extracted with Qiagen RNeasy Kit following manufacturer's instructions.
RNA sequencing library construction, quality control, and paired-end sequencing were performed by the UPMC Genome Center (Pittsburgh, Pennsylvania) according to their protocol.

treatment_protocol: Biological triplicates of each cell line were treated with 100µM fulvestrant (#1047, Tocris) dissolved in 100% ethanol or equal volume 100% ethanol for 24 hours.

value: T47D shESR1

value: No special type breast cancer cell line

value: Veh

tag: duration


title: ESR1-YAP1_shESR1_ICI2

value: ICI


title: ESR1-YAP1_shESR1_ICI1


title: ESR1-YAP1_shESR1_ICI3


title: ESR1-YAP1_shESR1_Veh2


title: ESR1-SOX9_shESR1_ICI3


title: ESR1-SOX9_shESR1_ICI2


title: ESR1-YAP1_shESR1_Veh1


title: TS13-20_tECM1_2

description:
TS13-20_tECM
SAMPLE 7


title: TS13-20_Collagen_2

description:
TS13-20_Collagen
SAMPLE 2


title: TS13-20_nECM_1

description:
TS13-20_nECM
SAMPLE 4


title: ESR1-SOX9_shESR1_ICI1


title: TS13-20_tECM3_2

description:
TS13-20_tECM
SAMPLE 13


title: TS13-20_tECM3_1

description:
TS13-20_tECM
SAMPLE 12


title: TS13-20_tECM1_3

description:
TS13-20_tECM
SAMPLE 8


title: TS13-20_Collagen_1

description:
TS13-20_Collagen
SAMPLE 1


title: TS13-20_tECM4_2

description:
TS13-20_tECM
SAMPLE 16


title: TS13-20_tECM2_2

description:
TS13-20_tECM
SAMPLE 10


title: TS13-20_Collagen_3

description:
TS13-20_Collagen
SAMPLE 3


title: TS13-20_tECM2_3

description:
TS13-20_tECM
SAMPLE 11


title: TS13-20_tECM2_1

description:
TS13-20_tECM
SAMPLE 9


title: ESR1-SOX9_shESR1_Veh2


title: TS13-20_tECM1_1

description:
TS13-20_tECM
SAMPLE 6


title: TS13-20_tECM3_3

description:
TS13-20_tECM
SAMPLE 14


title: TS13-20_nECM_2

description:
TS13-20_nECM
SAMPLE 5


title: TS13-20_tECM4_1

description:
TS13-20_tECM
SAMPLE 15


title: ESR1-LPP_shESR1_ICI2


title: ESR1-SOX9_shESR1_Veh3


title: ESR1-LPP_shESR1_ICI1


title: ESR1-LPP_shESR1_Veh2


title: ESR1-LPP_shESR1_Veh1


title: ESR1-LPP_shESR1_ICI3


title: ESR1-LPP_shESR1_Veh3


title: ESR1-DAB2_shESR1_ICI3


title: ESR1-DAB2_shESR1_ICI2


title: ESR1-SOX9_shESR1_Veh1


title: ESR1-DAB2_shESR1_Veh3


title: ESR1-DAB2_shESR1_ICI1


title: TS14-08_Collagen

description:
TS14-08_Collagen
SAMPLE 24


title: ESR1-DAB2_shESR1_Veh1


title: ESR1-∆CTD_shESR1_ICI3


title: ESR1-DAB2_shESR1_Veh2


title: ESR1-∆CTD_shESR1_Veh2


title: ESR1-WT_shESR1_ICI1


title: ESR1-∆CTD_shESR1_Veh3


title: ESR1-WT_shESR1_Veh3


title: ESR1-∆CTD_shESR1_ICI2


title: ESR1-WT_shESR1_ICI3


title: ESR1-WT_shESR1_ICI2


title: ESR1-WT_shESR1_Veh2


title: ESR1-∆CTD_shESR1_ICI1


title: S20

city: Chicago

first: Shashwat

last: Tripathi

address: 302 e Huron St

department: Neurosurgery

institute: Northwestern

description: 10x Genomics

data_processing:
Cell Ranger
Seurat
Assembly: hg38
Supplementary files format and content: Tab seperated and matrix

source_name: Brain

extract_protocol:
Patient tumors were graded pathologically by the study neuropathologists (CMH, NW) according to the World Health Organization classification [14]. At least 500 mg of the viable tumor was required to obtain enough for analysis and was processed within 30 min-1hour after resection. The normal brain was obtained from subjects as part of the planned surgical approach to gain access to a low-grade non-infiltrating glioma or during a planned super-total resection of adjacent regions that lacked T2/Flair abnormality on MRI imaging. The normal brain was sent for analysis separately from the tumor. The freshly resected tissue was processed in parallel both for a single cell suspension and formalin-fixed paraffin embedded (FFPE) analysis. For the former, the tissue was minced into small pieces using a scalpel, dissociated, and suspended using a Pasteur pipette in 10ml Iscove’s DMEM (IMDM; Iscove’s Modification of DMEM) 1X (Corning) containing 2% inactivated Fetal Bovine Serum (FBS; Sigma Aldrich) and Collagenase and DNase enzymes at final concentrations of 100μg/ml and 20units/ml, respectively. The prepared mixture was incubated for 35-40mins at 37°C with agitation. After tissue filtration using a 70-μm nylon cell strainer (BD Biosciences) and a brief centrifugation at 4°C, the pellet was resuspended in 20ml mix of 5.4ml of Percoll™ Plus (GE Healthcare) overlaid with 12ml of 1X Phosphate Buffered Saline (PBS) and 0.6ml of 10X PBS (Corning). The tube was centrifuged at 800gfor 10min at 4°C, with 9 acceleration and 0 deceleration. After centrifugation, the immune enriched cell pellet was collected, washed, stained with Trypan blue dye (Sigma-Aldrich), and counted using Countess II FL automated cell counter in a Countess cell counting chamber (Invitrogen). The FFPE slides were collected from the Neurological Surgery Tumor Bank (NSTB) of Northwestern University. Slides of tissue of 4 µm thickness were prepared, mounted on positively charged glass slides (Super Frost Plus microscope slides, ThermoFisher), and stored at room temperature for subsequent staining analysis. For each case, 1 H&E slide was reviewed, and tissue was segmented by a certified neuropathologist (CMH).
Single-cell sequencing was carried out using the chromium Next GEM Single Cell protocol (10x genomics). Post-library preparation cells were sequenced using the Illumina Novaseq

tag: disease

value: Normal


title: ESR1-∆CTD_shESR1_Veh1


title: S19

description: 10x Genomics


title: S21

description: 10x Genomics


title: S18

description: 10x Genomics

value: LGG


title: S17

description: 10x Genomics


title: S15

description: 10x Genomics


title: ESR1-WT_shESR1_Veh1


title: S13

description: 10x Genomics


title: S11

description: 10x Genomics


title: S9

description: 10x Genomics


title: S10

description: 10x Genomics


title: S8

description: 10x Genomics


title: S6

description: 10x Genomics


title: S4

description: 10x Genomics

value: HGG


title: S5

description: 10x Genomics


title: S3

description: 10x Genomics


title: S2

description: 10x Genomics


title: miRNA, placebo, D3 [HGKVFDSXY_104077-003-031_CACGATAT-GTTCAGAG_L002]

city: Leiden

first: Eleonora

last: Vianello

address: Albinusdreef 2

institute: Leiden University Medical Center

description: miRNA-seq

data_processing:
Adapters and indexes have been removed by using cutadapt v2.10.
Reads were aligned to GRCh38 by using bowtie2 v2.3.5.1.
Alignments were processed using samtools v1.9 to obtain a sorted bam-file which was used as input in HTSeq.count v0.13.0.
Counts were normalized by sequencing depth, dividing each sample with the column sums and multiplying them by 1 M. Baseline adjustment was performed individually by dividing the normalized data at each time point (day 1, 2, 3, and 7) by day 0 (e.g. day 1/day 0). All values were Log2-transfomed before further analyses. The R software v4.0.1 was used to perform normalization and baseline adjustment.
Assembly: GRCh38
Supplementary files format and content: csv file with normalized and log2 transformed counts

source_name: whole blood

extract_protocol:
WB-RNAs, including miRNAs, were isolated by using the PAXgene blood miRNA kit (PreAnalytiX). This kit guarantees the extraction of intracellular RNA and miRNA upon cell lysis and stabilization of intracellular RNA during whole blood collection in PAXgene blood RNA tubes (PreAnalytiX). The elutes were quantified with a Qubit fluorometer (ThermoFisher Scientific) by using the RNA Broad Range assay kit (ThermoFisher Scientific). RNA quality was assessed by using Agilent RNA (15nt) fragment analysis (Agilent).
Libraries were prepared using the NEBNextâ Multiplex Small RNA Library Prep Kit for Illumina (New England BioLabs) (Index Primers 1-48, #7560S). Their quality and yield were measured by Agilent HS NGS fragment analysis (Agilent). The final products have approximate size of 150 bp. The 1.1 nM libraries, derived from the WB RNAs, were sequenced using the NovaSeq 6000 sequencer with a 150 bp paired-end protocol. Between 9 and 41 million reads were obtained for each sample (average of 17 million reads per sample).

value: whole blood

value: placebo


title: miRNA, placebo, D3 [HGG2NDSXY_104077-003-031_CACGATAT-GTTCAGAG_L003]

description: miRNA-seq


title: OVCF, scRNAseq

first: Yude

last: Xu

state: Guangdong

address: No. 396, Tongfu Middle Road

institute: Guangzhou Red Cross Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
MT% < 20%;
Cell Gene Number < 10000;
Cell Gene Number > 200.
PCA and tSNE/UMAP analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Vertebral bone tissue

extract_protocol:
tissues  were dissociated to single cell.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

value: Vertebral bone tissue

tag: subject status

value: OVCF

value: percutaneous lumbar 4 vertebral balloon angioplasty


title: miRNA, placebo, D7 [HGKVFDSXY_104077-003-030_CACCGGAT-GTTCAGAG_L002]

description: miRNA-seq


title: KD, scRNAseq

value: KD

value: L2 vertebroplasty + percutaneous L1 and L3 pedicle screw internal fixation


title: S14

description: 10x Genomics

value: Brain


title: S12

description: 10x Genomics


title: miRNA, placebo, D7 [HGG2NDSXY_104077-003-030_CACCGGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HFKMYDSXY_104077-003-029_CAACTAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D0 [HGKVFDSXY_104077-003-027_ATTCCTAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D2 [HGKVFDSXY_104077-003-025_ACTGATAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D7 [HFKMYDSXY_104077-003-026_ATGAGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D2 [HGG2NDSXY_104077-003-025_ACTGATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D0 [HFKMYDSXY_104077-003-024_GGTAGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D0 [HGG2NDSXY_104077-003-027_ATTCCTAT-GTTCAGAG_L003]

description: miRNA-seq


title: S7

description: 10x Genomics


title: miRNA, placebo, D3 [HFKMYDSXY_104077-003-023_GAGTGGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D1 [HGKVFDSXY_104077-003-022_CGTACGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HFKMYDSXY_104077-003-021_GTTTCGAT-GTTCAGAG_L004]

description: miRNA-seq

value: rVSV{delta}G-ZEBOV-GP vaccine, dose 2*10^7


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HFKMYDSXY_104077-003-020_GTGGCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D1 [HGKVFDSXY_104077-003-028_CAAAAGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HFKMYDSXY_104077-003-019_GTGAAAAT-GTTCAGAG_L004]

description: miRNA-seq


title: S1

description: 10x Genomics


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HFKMYDSXY_104077-003-018_GTCCGCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HFKMYDSXY_104077-003-017_GTAGAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGKVFDSXY_104077-003-017_GTAGAGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D1 [HGG2NDSXY_104077-003-022_CGTACGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D7 [HFKMYDSXY_104077-003-016_CCGTCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D0 [HFKMYDSXY_104077-003-014_AGTTCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D1 [HGG2NDSXY_104077-003-028_CAAAAGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HFKMYDSXY_104077-003-015_ATGTCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D3 [HFKMYDSXY_104077-003-013_AGTCAAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D7 [HGKVFDSXY_104077-003-011_GGCTACAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D7 [HGG2NDSXY_104077-003-011_GGCTACAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D1 [HFKMYDSXY_104077-003-012_CTTGTAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D2 [HGKVFDSXY_104077-003-009_GATCAGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D3 [HFKMYDSXY_104077-003-010_TAGCTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D7 [HFKMYDSXY_104077-003-006_GCCAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D3 [HGG2NDSXY_104077-003-005_ACAGTGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HGG2NDSXY_104077-003-009_GATCAGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D0 [HFKMYDSXY_104077-003-007_CAGATCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D2 [HFKMYDSXY_104077-003-004_TGACCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D1 [HGKVFDSXY_104077-003-003_TTAGGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D1 [HGG2NDSXY_104077-003-003_TTAGGCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D0 [HGKVFDSXY_104077-003-002_CGATGTAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D0 [HGG2NDSXY_104077-003-002_CGATGTAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGKVFDSXY_104077-003-001_ATCACGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGG2NDSXY_104077-003-001_ATCACGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-096_TCGGCAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-096_TCGGCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-094_TCCCGAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-095_TCGAAGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHY2DSXY_104077-002-092_TATAATAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-094_TCCCGAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-002-092_TATAATAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-089_GACGACAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D1 [HFKMYDSXY_104077-003-008_ACTTGAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-002-093_TCATTCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-002-087_CTATACAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-002-087_CTATACAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-090_TAATCGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-002-088_CTCAGAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D3 [HGKVFDSXY_104077-003-005_ACAGTGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-091_TACAGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-086_CTAGCTAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-085_CGGAATAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-084_CCAACAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-085_CGGAATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-002-082_CATGGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-002-083_CATTTTAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGHY2DSXY_104077-002-083_CATTTTAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-080_CACTCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-081_CAGGCGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-079_CACGATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-076_CAAAAGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHY2DSXY_104077-002-077_CAACTAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-002-077_CAACTAAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-075_ATTCCTAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-076_CAAAAGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-002-088_CTCAGAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-075_ATTCCTAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-071_GAGTGGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-072_GGTAGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-074_ATGAGCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGHY2DSXY_104077-002-071_GAGTGGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-002-073R_ACTGATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-002-070_CGTACGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-069_GTTTCGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHY2DSXY_104077-002-070_CGTACGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D2 [HGH7GDSXY_104077-002-066R_GTCCGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D7 [HGH7GDSXY_104077-002-067_GTGAAAAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, placebo, D7 [HGHY2DSXY_104077-002-067_GTGAAAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-002-068_GTGGCCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D1 [HGH7GDSXY_104077-002-064_CCGTCCAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, placebo, D2 [HGH7GDSXY_104077-002-066R_GTCCGCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D0 [HGH7GDSXY_104077-002-063_ATGTCAAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, placebo, D3 [HGHY2DSXY_104077-002-065_GTAGAGAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D1 [HGHY2DSXY_104077-002-064_CCGTCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D0 [HGHY2DSXY_104077-002-063_ATGTCAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D2 [HGH7GDSXY_104077-002-061_AGTCAAAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, placebo, D2 [HGHY2DSXY_104077-002-061_AGTCAAAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D7 [HGHY2DSXY_104077-002-062_AGTTCCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, placebo, D3 [HGH7GDSXY_104077-002-065_GTAGAGAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, placebo, D0 [HGH7GDSXY_104077-002-058_TAGCTTAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-002-078_CACCGGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D1 [HGH7GDSXY_104077-002-059_GGCTACAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D0 [HGH7GDSXY_104077-002-058_TAGCTTAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-056_ACTTGAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-002-055_CAGATCAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-057R_GATCAGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D3 [HGH7GDSXY_104077-002-060_CTTGTAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-054_GCCAATAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-054_GCCAATAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D3 [HGH7GDSXY_104077-002-060_CTTGTAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-052_TGACCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGH7GDSXY_104077-002-053_ACAGTGAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGHY2DSXY_104077-002-055_CAGATCAT-GTTCAGAG_L004]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D7 [HGH7GDSXY_104077-002-052_TGACCAAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D2 [HGH7GDSXY_104077-002-051_TTAGGCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D3 [HGH7GDSXY_104077-002-050R_CGATGTAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D7 [HGH7GDSXY_104077-002-062_AGTTCCAT-GTTCAGAG_L001]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D1 [HGH7GDSXY_104077-002-049R_ATCACGAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, rVSVΔG-ZEBOV-GP, D0 [HGJFJDSXY_104077-002-048_TCGGCAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D2 [HGJFJDSXY_104077-002-046_TCCCGAAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D3 [HGKVFDSXY_104077-002-045_TCATTCAT-GTTCAGAG_L003]

description: miRNA-seq


title: miRNA, placebo, D3 [HGJFJDSXY_104077-002-045_TCATTCAT-GTTCAGAG_L002]

description: miRNA-seq


title: miRNA, placebo, D7 [HGJFJDSXY_104077-002-047_TCGAAGAT-GTTCAGAG_L002]

description: miRNA-seq