title: non-vein endothelium cells, Control, Day5 rep1

first: zhujuan

last: huang

address: No. 382, east waihuan road, panyu district, GuangZhou city, GuangDong province Medical college of south China university of technology, panyu university town, Guangzhou city

institute: South China University of Technology

data_processing:
Filtering of Clean Reads by fastp (version 0.18.0).The parameters were as follows:1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Correlation analysis was performed by R. Correlation of two parallel experiments
Principal component analysis (PCA) was performed with R package gmodels (http://www.r- project.org/) in this experience;RNAs differential expression analysis was performed by DESeq2;
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: Caudal hematopoietic tissue

extract_protocol:
Non-vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tg(kdrl:GFP;lyve1b:DsRed) CHT,collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).
The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: Caudal hematopoietic tissue

tag: cell type

value: non-vein endothelium cells

value: Wildtype

value: no treatment


title: vein endothelium cells, Day5 rep1

status: Public on Nov 16 2023

type: SRA

city: Guangzhou

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue

value: vein endothelium cells

tag: genotype

tag: treatment


title: non-vein endothelium cells, Control, Day5 rep2


title: MB91

type: genomic

city: Southampton

first: Matthew

last: Hewitt

state: Hampshire

address: Institute of developmental sciences, 216 Tremona Road

department: Human Development and Health

country: United Kingdom

institute: University of Southampton

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol

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

data_processing:
The processing of myoblast Infinium Human MethylationEPIC data and all statistical analysis was conducted in R (v3.4.2).
Average Beta or normalized (provide the normalization method) Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Myoblast gDNA isolated and cultured from vastus lateralis muscle tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (gDNA) was extracted from actively proliferating myoblasts using the GenEluteTM Mammalian Genomic DNA miniprep Kit (Merck) following manufacturer’s instructions.

tag: Sex

value: Male


title: 16HBE ex14 + HGF [257236334397_S01_GE1_107_Sep09_2_2]

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: ex14 treated by HGF

hyb_protocol: Agilent-072363 Whole Human Genome Microarray 8x60 v3 were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: 16HBE ex14 + HGF

label_protocol: manufacturer's instructions

growth_protocol: MEM, 10% FBS and 1% Zell-Shield, 37°C, 5% CO2

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: 16HBE WT and 16HBE ex14 were starved (0% FBS) during 2 hours and next stimulated 24 hours by HGF (20 ng/ml)

tag: cell line

tag: agent

value: HGF


title: 16HBE ex14 [257236334397_S01_GE1_107_Sep09_2_4]

description: ex14 non treated

source_name: 16HBE ex14


title: 16HBE ex14 [257236334397_S01_GE1_107_Sep09_1_1]

description: ex14 non treated


title: 16HBE WT [257236334397_S01_GE1_107_Sep09_1_4]

description: WT non treated

source_name: 16HBE WT

value: WT


title: 16HBE ex14 + HGF [257236334397_S01_GE1_107_Sep09_1_3]

description: ex14 treated by HGF


title: whole cell, set1d, 30 C, rep2

city: Winston-Salem

first: Ke

last: Zhang Reid

state: NC

address: 1834 Wake Forest Rd

country: USA

institute: Wake Forest University

data_processing:
Reads were first trimmed of adapters using Trimmomatic v 0.39 under the default settings using adaptors from TruSeq2-PE.fa
RNA-Seq reads for each sample were aligned to the S. pombe reference genome ASM294v2 using STAR
Aligned reads were quantified using FeatureCounts with options -t gene -o fraction
Assembly: ASM294v2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Schizosaccharomyces pombe

source_name: whole cell

extract_protocol:
Quick-RNA Miniprep Kit (Zymo Research, R1054) following manufacturer protocols
Novogene Plant and Animal Eukaryotic Strand Specific mRNA (WOBI) sequencing following standard protocol

value: whole cell


title: 16HBE YY + HGF [257236334397_S01_GE1_107_Sep09_1_2]

description: WT treated by HGF

source_name: 16HBE YY + HGF


title: MB157

value: Female


title: MB159


title: 1008498_day 17

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

data_processing:
Illumina NextSeq 500 generated BCL files that were converted to FastQ files
FastQ files were demultiplexed using bcl2fastq2
Reads were quality filtered and adapter trimmed in silico using Cutadapt
miRDeep2 was used to generate miRNA expression count data
Data was normalized to CPM values using TMM normalization
Assembly: Sus scrofa reference genome assembly using Bowtie v2.2.3.0
Supplementary files format and content: Text file with miRNA count data

organism: Sus scrofa

source_name: Plasma

extract_protocol:
Blood samples were taken from the animals and centrifuged to obtain plasma
TruSeq small RNA Sample Preparation kit was used for library construction

value: Plasma

tag: timepoint

value: day 17

tag: radiation dose

value: 2.2 Gy Total body irradiation

tag: sample


title: 1008498_day 7

value: day 7


title: 1008498_day 20

value: day 20


title: MB160


title: whole cell, lsd1dHMG, 37 C, rep2


title: MB156


title: whole cell, set1d, 37 C, rep2


title: 1008498_day 3

value: day 3


title: 1008498_day 10

value: day 10


title: PA2

city: Nanjing

first: Xue

last: Zhang

state: Jiangsu

address: 1 Weigang

institute: Nanjing Agricultural University

library_source: genomic

data_processing:
Raw data was stored in FASTQ format, including the base sequence and corresponding quality  information. Trimmomatic (v0.36) was used to remove adaptor-polluted or low-quality bases, and  reads too short ( < 36 nt) were filtered out to get the clean data.
Clean data was mapped to reference  genome by Bowtie2, and visualized by IGV
Peaks corresponding  to the open region in genome were detected by MACS2
significantly different peaks between  samples were acquired using Manorm
he enrichment analysis of GO term  (http://geneontology.org/) or KEGG pathway (http://www.kegg.jp/) was based on hypergeometric  test with the threshold q < 0.05, to find the significant enrichment of detected genes
Genome_build: Sus_scrofa.Sscrofa11.1.90.chr
Supplementary_files_format_and_content: bw

source_name: parthenogenetic activation embryos

extract_protocol:
After removing the zona pellucida, oocytes or embryonic cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al and Jingyi Wu et al. with slightly modification

value: embryo

tag: development stage

value: 10 h after activation


title: 1008498_day 14

value: day 14


title: PA1


title: whole cell, WT, 37 C, rep2


title: MB155


title: whole cell, WT, 30 C, rep2


title: SCNT2

source_name: somatic cell nuclear transfer embryos


title: 1008498_day 1

value: day 1


title: whole cell, set1d, 37 C, rep1


title: SCNT1


title: MB154


title: MB153


title: 1008498_day 0

value: day 0


title: whole cell, set1d, 30 C, rep1


title: GV2

source_name: oocytes at germinal vesicle stage

value: oocyte

value: GV


title: 1008498_day -7

value: day -7


title: whole cell, lsd1dHMG, 30 C, rep2

value: whole cell


title: RNA-seq of C. elegans: adult day 5 N2 hermaphrodites (rep5)

status: Public on Nov 17 2023

city: Cambridge

first: Laura

last: Chipman

state: MA

address: 1 Portland St

institute: Pfizer

data_processing: Reads were aligned to the C. elegans genome WBcel282 assembly using STAR and the average percent of uniquely mapped reads was 94% (Dobin et al. 2013). Aligned reads were sorted using Samtools (Danecek et al. 2021) and reads were then quantified using featureCounts using WBcel282 gene annotations (Liao, Smyth, and Shi 2014). Differential expression was calculated using DESeq2 (Love, Huber, and Anders 2014). Genes with +/- 1 Log2FC, a basemean of at least 10, and adjusted p-value of < 0.05 were considered significantly mis-regulated.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Adult C. elegans were separated from eggs and progeny daily by washing plates with M9 into conical tubes and allowing the adults to settle by gravity for a few minutes on a bench top. The supernatant containing larvae and eggs was then removed, and this process was repeated 3-15 times until eggs and larvae were no longer visible.

extract_protocol: RNA was isolated from wildtype (N2), miR-238(n4112), miR-239a(ap439), and miR-239b(ap432) day 5 adults. Adult C. elegans were separated from eggs and progeny on a daily basis by washing plates with M9 into conical tubes and allowing the adults to settle by gravity for a few minutes on a bench top. The supernatant containing larvae and eggs was then removed, and this process was repeated 3-10 times until eggs and larvae were no longer visible.Three independent poly(A) selected RNA-seq libraries were prepared from each strain for sequencing with the Illumina TruSeq mRNA Library Prep Kit. cDNA libraries were sequenced on an Illumina NovaSeq 6000.

value: whole organism

tag: strain

tag: developmental stage

value: adult day 5

tag: fraction

value: polyA RNA


title: MB152

value: Female


title: 1008498_day -1

value: Plasma

value: day -1

value: 2.2 Gy Total body irradiation


title: 1008064_day 7

value: day 7


title: MB10


title: whole cell, WT, 37 C, rep1

value: WT


title: MB61

value: Male


title: MB150


title: whole cell, lsd1dHMG, 30 C, rep1


title: A. fumigatus wild type, 3h fludioxonil, biol rep 4

city: Jena

first: Tongta

last: Sae-Ong

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (Leibniz-HKI)

data_processing:
Sequence reads were preprocessed using the GEO2RNAseq pipeline (DOI: https://doi.org/10.1101/771063), including the steps below:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36 (parameters- -phred33, ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:15:25, and MINLEN:30)
Trimmed sequence reads were filtered rRNA using SortMeRNA v.2.1
Non-rRNA sequence reads were mapped to Aspergillus fumigatus Af293 using HISAT2 v.2.1.0 (parameters- -k 2, --no-unal, --no-mixed, and –no-discordant)
Reads were counted per feature using Rsubread’s feature Counts v.1.20.6 (featureCounts: parameters- isGTFAnnotationFile=TRUE, GTF.attrType='gene_id', GTF.featureType='exon', strandSpecific=0, isPairedEnd=TRUE, requireBothEndsMapped=TRUE, useMetaFeatures=TRUE, allowMultiOverlap=FALSE, and countMultiMappingReads=FALSE)
Read counts were normalized by the “Median by-Ratio Normalization (MRN)” method from EBSeq
Assembly: Aspergillus fumigatus Af293
Supplementary files format and content: An excel files included a matrix of read count values for every samples (counts.xls)
Supplementary files format and content: An excel file includes a matrix of normalized read counts for every samples (mrn.xls)

organism: Aspergillus fumigatus

source_name: Strain AfS35

growth_protocol: A. fumigatus strains were grown in liquid AMM (inoculum 1x106/ml) for 18 hours before treatment

extract_protocol:
RNA was isolated from ground mycelium with the Qiagen Plant RNeasy Mini Kit (Hilden, Germany) according to the manufacturer’s instructions, quantified at 260 nm with a NanoDrop ND-1000 UV VIS spectrophotometer
Illumina TruSeq RNA sample preparation kit

treatment_protocol: A. fumigatus cultures were treated by the addition of fludioxonil (in DMSO) with a final concentration of 2 µg/ml for 1 or 3 hours

value: Strain AfS35

value: mycelium

value: 2microgram/ml fludioxonil

tag: time

value: 3 h


title: whole cell, WT, 30 C, rep1


title: 1008064_day 20

value: day 20


title: 1008064_day 3

value: day 3


title: A. fumigatus wild type, 3h fludioxonil, biol rep 3


title: MB148


title: 1008064_day 17

value: day 17


title: A. fumigatus wild type, 3h fludioxonil, biol rep 1


title: A. fumigatus wild type, 3h fludioxonil, biol rep 2


title: Multiplex_pancreas_organoids #2 CMO

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v6.1.1)
cellranger mkfastq was used for fastq generation. Gene expression data was stored in the *GEX* files and Cell multiplexing oligo data was stored in the *CMO* files.
cellranger multi was used to separate samples based on their cell multiplexing oligo (CMO), align reads to the 10X pre-build mouse reference genome (mm10) and extract gene expression UMI counts matrix.
Assembly: mm10
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

organism: Mus musculus

source_name: Pancreas

growth_protocol: The organoids were cultured in mouse complete culture medium, which include Advanced DMEM/F12 medium supplemented with HEPES (1x, Invitrogen), Glutamax (1x, Invitrogen), penicillin/streptomycin (1x, Invitrogen), B27 (1x, Invitrogen), N-acetyl-L-cysteine (1.25 mM, Sigma), 10% R-Spondin1-Conditioned Medium, mouse Noggin recombinant protein (mNoggin) (0.1 μg/mL, Peprotech), mouse epidermal growth factor (EGF, 50 ng/ml, Peprotech), human Gastrin (10 nM, Sigma), fibroblast growth factor 10 (FGF10, 100 ng/ml, Prepotech), Nicotinamide (10 mM, Sigma), A83-01 (0.5 μM, Tocris) and Y-27632 (10.5μM). KSC and KPSC organoids can be cultured in mouse complete culture medium without mNoggin and A83-01, because of loss function of TGF-β. organoids were passaged about every 5 days when the cultures reached complete confluency. Organoids were dissociated into single cells or small clusters by enzymatic dissociation with 0.05% Trypsin-EDTA (Thermo Fisher) for 9 minutes in 37° water bath. The basial medium, Advanced DMEM/F12 medium supplemented with HEPES, Glutamax and penicillin/streptomycin, was used to neutralize trypsin. The cells were spin down and suspended in GFR Matrigel with a 1:6-1:8 passage ratio to seed again.

extract_protocol:
Cultured organoids were collected from 24 well plates and dissociated with Accutase to obtain single cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Pancreas

value: pancreas organoids

value: pancreas

value: wild type or KRASG12D (KC), KRASG12D; Tp53R172H (KPC), KRASG12D; SMAD4-/- (KSC) and KRASG12D; Tp53R172H and SMAD4-/- (KPSC)

value: treated with or without perhexiline


title: Multiplex_pancreas_organoids #2 GEX

description: 10x Genomics


title: MB146

value: Female


title: A. fumigatus wild type, 1h fludioxonil, biol rep 4

value: 1 h


title: 1008064_day 10

value: Plasma

value: day 10

value: 2.2 Gy Total body irradiation


title: MB147


title: A. fumigatus wild type, 1h fludioxonil, biol rep 3

value: Strain AfS35


title: 1008064_day 14

value: day 14


title: GV1

value: oocyte

value: GV


title: MI_RG3

city: shanghai

first: min

last: chen

address: dongfang road 1678

institute: Shanghai children's Medical Center

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

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: Pre-treating mice with RG(1ml/20g,B.Braun) or saline before MI surgery

value: heart

value: male

value: WT

tag: age

value: Myocardial infarction,Ringerfundin


title: whole cell, lsd1dHMG, 37 C, rep1

value: whole cell


title: A. fumigatus wild type, 1h fludioxonil, biol rep 2

value: mycelium

value: 2microgram/ml fludioxonil


title: MI_RG2


title: MB145


title: MI_RG1


title: vein endothelium cells, Day5 rep2

value: Caudal hematopoietic tissue

value: vein endothelium cells

value: Wildtype

value: no treatment


title: A. fumigatus wild type, 1h fludioxonil, biol rep 1

value: 1 h


title: 1008064_day 1

value: Plasma

value: day 1

value: 2.2 Gy Total body irradiation


title: MB143

value: Female


title: A. fumigatus wild type, untreated, biol rep 4

value: Strain AfS35

value: No treatment

value: 0 h


title: 1008064_day -7

value: day -7


title: 1008064_day 0

value: day 0


title: MI2

value: heart

value: male

value: WT

value: Myocardial infarction,saline


title: A. fumigatus wild type, untreated, biol rep 3

value: mycelium


title: MB142


title: MI1


title: MB141


title: MB140


title: A. fumigatus wild type, untreated, biol rep 1


title: 1000667_day 7

value: day 7


title: A. fumigatus Dskn7, 3h fludioxonil, biol rep 4

value: 2microgram/ml fludioxonil

value: 3 h


title: Sham2

value: sham operation


title: MB139


title: 1000667_day 20

value: Plasma

value: day 20


title: MB138

value: Female


title: Sham1


title: A. fumigatus Dskn7, 3h fludioxonil, biol rep 3

value: Strain AfS35


title: PVR 9 BL Maraviroc

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
To generate gene expression matrix, fastq files were processed and mapped to the GRCm39.109 reference genome using Parse Biosciences SplitPipe v1.0.4 with default parameters (Parse Biosciences, Seattle, WA). The downstream analysis was performed using the R 4.2.2 and Seurat v4.3.0 R package (Hao et al 2021). Low-quality cells with less than 200 genes detected and all genes expressed in less than 3 cells were removed, leaving 69,962 cells and 37,725 genes for further analysis. Data was normalized using Seurat’s NormalizeData function with LogNormalize as a method and a scale factor equal to 10,000. Principal Component Analysis was performed on a submatrix of the top 2,000 most variable genes, using the function FindVariableGenes from the Seurat package. The number of top Principal Components (PC) was evaluated by the elbow method keeping 33 PCs for clustering and data visualization. The batch effect between samples was removed using the package Harmony v0.1.1 (Kursunsky et al. 2019). The cells were clustered using a shared nearest neighbor modularity optimization-based clustering algorithm (FindClusters in the Seurat package). To visualize cells in two dimensions the Uniform Manifold Approximation and Projection was applied (Becht et al. 2019). The cluster-specific genes were computed using FindAllMarkers from the Seurat package, using the MAST test with the number of Unique Molecular Identifiers detected as a latent variable (Finak et al 2015). The same test was used to compute differentially expressed genes between genotypes or treatment groups within cell clusters. Cell clusters were annotated by assessing known cell-type-specific markers. All plots were created using ggplot v3.4.1. Labels in the volcano plots were created using ggrepel v0.9.3.
Assembly: GRCm39

molecule: polyA RNA

source_name: retina

growth_protocol: All mice were housed under a standard 12-hour light (≤150 lux)/12-hour dark cycle and bred using standard procedures.

extract_protocol:
Eyes were enucleated for retinal tissue isolation. After removing the anterior chamber and lens, the retina was dissected from the posterior eye cup. Then, the retinal cells were dissociated using the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions.
8 sublibraries were generated and sequenced independently on Illumina NovaSeq6000 at an average sequencing depth of 50,000 reads/cell, for a projected total of 5 billion reads for the entirety of the 100,000 cell barcoded library. Reads from identical cells from each of the 8 sublibraries were consolidated during analysis and processing of raw reads.

treatment_protocol: Light damage was induced in photosensitive Abca4-/-Rdh8-/- and Abca4PV/PVRdh8-/- mice by exposure to white light delivered at 10,000 lux (150-W spiral lamp, Commercial Electric, Cleveland, OH) for 30 min. Mice were dark-adapted 24 hr prior to photobleaching, and pupils were dilated with 1% ophthalmic tropicamide 30 min prior to light exposure. For maraviroc and DMSO (vehicle) treatments prior to bleaching, all drug/ vehicle treatments were injected interperitoneally in 60 μL volumes. Maraviroc was dissolved in 60 μL DMSO and administered interperitoneally at 60 mg/kg for ech of the maraviroc-treated animals. All drug/ vehicle treamtents were given approximately 30 minutes before bleaching.

tag: age (weeks)

value: Abca4PV/PVRdh8-/- (C57BL/6J)

value: Bleached and Maraviroc-treated


title: MB144


title: 1000667_day 17

value: day 17

value: 2.2 Gy Total body irradiation


title: A. fumigatus Dskn7, 3h fludioxonil, biol rep 2

tag: cell type


title: 1000667_day 14

tag: tissue

value: day 14


title: MB136


title: 1008064_day -1

value: day -1


title: PVR 8 BL Maraviroc


title: MI3

value: heart

value: male

tag: genotype

value: WT


title: A. fumigatus wild type, untreated, biol rep 2

value: mycelium

tag: treatment

value: No treatment

value: 0 h


title: PVR 7 BL Maraviroc


title: MB135

tag: Sex


title: A. fumigatus Dskn7, 3h fludioxonil, biol rep 1

tag: cell line

value: 2microgram/ml fludioxonil

value: 3 h


title: 1000667_day 1

value: Plasma

value: day 1


title: A. fumigatus Dskn7, 1h fludioxonil, biol rep 4

value: Strain AfS35

value: 1 h


title: 1000667_day 10

value: day 10


title: MB48

value: Female


title: DKO (Leu) 9 BL Maraviroc Treated

value: Bleached and Maraviroc-treated


title: A. fumigatus Dskn7, 1h fludioxonil, biol rep 3


title: 1000667_day 0

value: day 0

value: 2.2 Gy Total body irradiation


title: MB133


title: Sham3

value: heart

value: sham operation


title: 1000667_day 3

value: day 3


title: MB132


title: DKO (Leu) 7 BL Maraviroc Treated


title: A. fumigatus Dskn7, 1h fludioxonil, biol rep 2

value: mycelium


title: 1000667_day -7


title: MB129


title: 1000667_day -1


title: WT-8 BL Maraviroc Treated


title: A. fumigatus Dskn7, 1h fludioxonil, biol rep 1


title: WT-9 BL Maraviroc Treated


title: human umbilical cord 10, induced stage, S4

city: Nanchang

first: Jianping

last: Liu

address: Building 1, Central University

institute: The Second Affiliated Hospital of Nanchang University

data_processing:
After library preparation and pooling of different samples, the samples were sequenced using an Illumina sequencer. Typically, lncRNA-seq uses PE150 (paired-end 150nt) sequencing to obtain 12G raw data.
Low-quality bases from raw reads were trimmed using the FASTX-Toolkit (v.0.013; http: // hannonlab.chsl.edu/fastx _toolkit/ ). The clean reads were evaluated using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Clean reads were aligned to the human GRch38 genome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) using HISAT2 （http://ccb.jhu.edu/software/hisat2;Kim D et al.,2015）
uniquely mapped reads were used to calculate the read number and fragments per kilobase of exon per million fragments mapped (FPKM) for each gene. The expression levels of the genes were evaluated by FPKM.
DESeq2 software, which is specifically used to analyze the differential expression of genes (DEGs), was used to screen the RNA-seq data for DEGs
Assembly: GRch38
Supplementary files format and content: gene_description.txt includes raw counts and RPKM values for each Sample
Supplementary files format and content: lncRNA_description.txt includes raw counts and RPKM values for each Sample

source_name: umbilical cord

growth_protocol: The UC-MSCs were cultured in ḁ-MEM complete medium, containing 10% foetal bovine serum, and 1% penicillin and streptomycin in a humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
Total RNA was extracted at each stage using TRIzol reagent®. 1.5ug of total RNA was used for the construction of sequencing libraries.
The RNA library for lncRNA-seq was prepared using rRNA depletion and the strand  method.

treatment_protocol: For induction, the medium was replaced with stage 1 medium containing DMEM:F12 supplemented with 10% FBS, 1% penicillin and streptomycin,10 mM nicotinamide, 20 ng/ml EGF, 50 µM β-mercaptoethanol and 4 nM  Activin A for 3 d. On the fourth day, at stage 2, the medium was replaced with media containing the same supplements as those in the stage 1 medium, but lacking Activin A and β-mercaptoethanol. The cells were then incubated for another 5 d. On the ninth day, the media was changed to stage 3 media containing DMEM:F12 (1:1) with supplemented 2% FBS, 1% penicillin and streptomycin, 20 ng/ml bFGF, 100x ITS, 10 nM exendin-4, and 10 mM NA, and the cells were cultured for another 7 d. On the sixteenth day, at stage 4, the medium was replaced with media containing the same supplements as those in stage 3, but lacking the 2% FBS supplement. The cells were allowed to mature in this medium for another 7 d. Changes in morphology were observed under a light microscope during differentiation.

value: umbilical cord

value: umbilical cord mesenchymal stem cell

tag: Stage

value: induced stage, S4


title: WT-7 BL Maraviroc Treated


title: A. fumigatus Dskn7, untreated, biol rep 3

value: No treatment

value: 0 h


title: MB2


title: MB122


title: PVR 5 BL Vehicle

value: Abca4PV/PVRdh8-/- (C57BL/6J)

value: Bleached and DMSO-treated


title: human umbilical cord 9, induced stage, S4


title: MB128


title: A. fumigatus Dskn7, untreated, biol rep 2

value: Strain AfS35


title: A. fumigatus Dskn7, untreated, biol rep 4


title: PVR 4 BL Vehicle


title: A. fumigatus Dskn7, untreated, biol rep 1


title: human umbilical cord 8, induced stage, S3

value: induced stage, S3


title: PVR 6 BL Vehicle


title: DKO (Leu) 8 BL Maraviroc Treated


title: MB124

value: Female


title: human umbilical cord 7, induced stage, S3


title: MB121


title: A. fumigatus DtcsC, 3h fludioxonil, biol rep 4

value: 2microgram/ml fludioxonil

value: 3 h


title: human umbilical cord 5, induced stage, S2

value: induced stage, S2


title: human umbilical cord 6, induced stage, S2


title: A. fumigatus DtcsC, 3h fludioxonil, biol rep 3


title: MB81

value: Male


title: human umbilical cord 4, induced stage, S1

value: induced stage, S1


title: A. fumigatus DtcsC, 3h fludioxonil, biol rep 2


title: DKO (Leu) 6 BL Vehicle


title: DKO (Leu) 5 BL Vehicle


title: MB79


title: A. fumigatus DtcsC, 3h fludioxonil, biol rep 1


title: human umbilical cord 2, induced stage, S0

value: induced stage, S0


title: MB68


title: DKO (Leu) 4 BL Vehicle


title: WT-4 BL Veh Treated


title: MB67


title: WT-6 BL Veh Treated


title: human umbilical cord 1, induced stage, S0


title: MB80


title: MB78


title: A. fumigatus DtcsC, 1h fludioxonil, biol rep 4

value: mycelium

value: 1 h


title: MB69


title: PVR 3 UB

value: Untreated, unbleached


title: MB66


title: Hashing reads for scGEX-2 & scBCR-2 (FA028, FA053, FA011)

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
GRCh38
Compressed tar files contain output from CellRanger, as well as sample-level metadata and sample hashing information.

source_name: Peripheral Blood

extract_protocol:
Peripheral blood was collected in heparin tubes (BD, #367874) and processed within 24 hours. Blood was spun at 1,500 rpm for 10 min. The plasma layer was collected and stored at -80°C. PBMCs were separated by Ficoll-Paque Plus density gradient centrifugation (Sigma-Aldrich, #GE17-1440-02) using Leucosep tube (Grainer Bio-One, #227288) following the manufacturer’s instructions. After the isolation, the PBMCs were counted and resuspended in 500 ul of 5% AB serum in RPMI and 500 ul of 20% DMSO in AB serum at 0.5 – 10 x 106 PBMCs per cryovial and cryopreserved.
10X Genomics libraries:B cells were isolated from 17 million to 100 million PBMC from 5 peanut allergic children with sIgE>100 and 3 non-allergic children by EasySepTM Human B cell Isolation Kit (STEMCELL technologies, #17954). Hash tagged antibodies were added to 3 million B cells from each sample. B cells from 2 peanut allergic subjects were combined in experiment 1. In experiment 2, B cells from 3 non-allergic subjects were combined, and B cells from 3 non-allergic children were combined. The cells were then stained with BV421 anti-human CD19 and FITC anti-human CD27 antibodies and CD19+CD27+ memory B cell populations were sorted on a FACSAria (BD). After confirming cell number and viability, B cells were run on a Chromium 10X controller using 5’ chemistry (10X Genomics) in one lane (experiment 1) or two lanes (experiment 2) with an expected recovery rate of 10,000 cells per lane, according to the manufacturer’s instructions. Libraries were generated and run on a HiSeq2500 apparatus.  PacBio Libraries: Ara h 2 multimers were generated by associating biotinylated Ara h 2 with PE-labeled streptavidin or AF647-labeled streptavidin. Similarly, detoxified diphtheria toxin (DT) (CRM197, PFENEX Biopharmaceuticals) was used to generate DT multimers. Ara h 2 (or DT) binding B cells were sorted into 96 well plates with lysis buffer containing RNAse inhibitor, dNTPs and oligo dT-VN30 anchored with template switch oligo sequence (Table S4). Plates were flash frozen in dry ice and stored at -80°C. Plates were thawed on ice, then oligo dT was added and annealing was performed at 70°C for 5 min. cDNA synthesis and cDNA amplification was performed with template switching oligo (TSO) using template switching RT enzyme mix (NEB) according to the manufacturer’s instruction. The first PCR was performed to amplify BCR heavy and light chains using outer primers targeting human immunoglobulin constant regions (IgG, IgM for heavy chains, kappa and lambda for light chains) and TSO inner primer (Table S4), respectively. After cleaning up the PCR products, BCR heavy and light chains were further amplified with inner primers with plate and row specific ID (5’) and column specific ID (3’) to enable the identification of BCR sequences derived from each well (Table S4). Afterwards, all PCR products were combined as one library. PacBio sequencing was performed to obtain long amplicon reads to cover 500 to 1000 bp. All PCR reactions were performed using NEBNext UltraTM II Q5 master mix (NEB).
BCR sequence data from 10X Genomics scRNA-seq + BCR sequencing began with the filtered V(D)J contigs from Cell Ranger version 3.1. To obtain V and J gene assignments, these contigs were aligned to the IMGT GENE-DB germline reference allele database (obtained 8/3/2019)43. Non-productive heavy and light chain BCR sequences were removed. BCRs were annotated by B cell subtype based on matching their single cell barcodes to the gene expression information. Only cells that had both gene expression and BCR sequence data were retained. In cells with multiple heavy chains, only one heavy chain with the highest unique molecular identifier count was retained. In the event of a tie, the first heavy chain identified was retained.
For BCR sequencing data from sorted single cell PacBio sequencing data, adaptor ligation, sequencing reactions, and initial sequence processing were conducted at GENEWIZ, LLC/Azenta US, Inc (South Plainfield, NJ, USA) using standard PacBio circular consensus sequence (CCS) tools and guidelines. Further processing was performed using presto v0.6.244. To remove reads too short to likely contain functional BCRs and associated constant regions, reads shorter than 500bp were removed. After initial processing, PacBio BCR sequence reads were assembled into consensus sequences. As with 10X Genomics BCR sequence data, consensus sequences were aligned to the IMGT GENE-DB database43 to obtain V and J germline annotations. Non-productive heavy and light chain BCR sequences were removed.
BCRs from both 10X Genomics and PacBio were processed using the Immcantation suite.

value: Peripheral Blood

value: B-Lymphocyte


title: A. fumigatus DtcsC, 1h fludioxonil, biol rep 3


title: human umbilical cord 3, induced stage, S1

value: umbilical cord

value: umbilical cord mesenchymal stem cell


title: Hashing reads for scGEX-1 & scBCR-1 (HC013, HC017, HC020)


title: PVR 2 UB

value: Abca4PV/PVRdh8-/- (C57BL/6J)


title: A. fumigatus DtcsC, 1h fludioxonil, biol rep 1

value: Strain AfS35


title: A. fumigatus DtcsC, untreated, biol rep 3

value: No treatment

value: 0 h


title: PVR1 UB redo


title: WT-5 BL Veh Treated

value: Bleached and DMSO-treated


title: Hashed scBCR sample (FA007, FA048)


title: Hashing reads for scGEX-3 & scBCR-3 (FA007, FA048)


title: A. fumigatus DtcsC, untreated, biol rep 2


title: A. fumigatus DtcsC, 1h fludioxonil, biol rep 2

value: 2microgram/ml fludioxonil


title: MB64

value: Female


title: Hashed scBCR sample (FA028, FA053, FA011)


title: DKO (Leu) 3 UB


title: DKO (Leu) 2 UB


title: MB60


title: MB59

value: Male


title: MB58


title: Hashed scGEX sample (FA007, FA048)


title: WT-2 UB


title: Hashed scBCR sample (HC013, HC017, HC020)


title: Hashed scGEX sample (HC013, HC017, HC020)


title: WT-3 UB


title: MB57


title: MB65


title: siRNA-3_48H

city: Storrs

first: Shipra

last: Malik

state: CT

address: 69 North Eagleville Road, Unit 3092

department: Pharmaceutical Sciences

institute: University of Connecticut

data_processing:
Read trimming: Trimmomatic, -l 45, q 25
Mapping: hisat2/2.2.1, Index=GRCh38
File format conversion: samtools/1.7
Feature count: htseq/0.11.0, htseq-count -s no -r pos -t exon -i gene_id -f bam,
Data counts were analysed with DESeq2 in R
Assembly: GRCh38
Supplementary files format and content: Nomalised counts in CSV file

source_name: Bone marrow

growth_protocol: U2932 cells were grown in RPMI medium (ATCC) supplemented with 10% fetal FBS, 1% Pen-Strep and cultured at 37 °C with 5% CO2 in a humidified chamber.

extract_protocol:
Total RNA from each sample was extracted using the Quigen RNeasy  Kit.
Total RNA was extracted after 48 hours. Total RNA was extracted from the collected cell pellets and submitted for RNA sequencing analysis. Illumina TruSeq stranded total RNA and mRNA was used for library preparation. The samples were then sequenced using Illumina NextSeq 500.

treatment_protocol: U2932 cells were seeded in 24-well plates at a density of 200,000 cells/well.  gPNA2 (8mM) were added to cells and incubated for 48 and 72 h. 5x10^6 U2932 cells were also transfected with siRNA (500nM) using electroporation for 48 hours.

value: Bone marrow

value: DLBCL

value: cmyc knockdown

value: siRNA


title: Hashed scGEX sample (FA028, FA053, FA011)


title: siRNA-4_48H


title: MB55

source_name: Myoblast gDNA isolated and cultured from vastus lateralis muscle tissue


title: ChIP-Seq_NtrX-HA_Caulobacter_crescentus_CB15_ntrX::ntrX-HA

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

data_processing:
Base calling: NextSeq Control Software 4.0.2.7, RTA 2.11.3, bcl2fastq2.17 v2.17.1.14
Read Quality: FastQC (Galaxy Version 0.74+galaxy0), FASTQ Trimmer (Galaxy Version 1.1.5)
Alignment: Bowtie2 (Galaxy Version 2.4.5+galaxy1)
Peak calling: MACS2 (Galaxy Version 2.2.7.1+galaxy0 , No broad regions option) relative to the total input DNA samples. The q-value (false discovery rate, FDR) cut-off for called peaks was 0.05.
Assembly: ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.47.2 (Braham Bionformatics Institute)
Supplementary files format and content: Caulobacter crescentus NA1000 (NC_011916.1)
Supplementary files format and content: The xlsx file reporting NtrX-HA ChIP-Seq RPM normalized profiles was generated by SeqMonk software. The sheet is organized in columns as follows: column 1: Start (bp); column 2: End (bp); column 3: Feature; column 4: Description; column 5: Feature Strand; column 6: Feature Type; column 7 and 8: NtrX-HA ChIP-Seq profiles (normalized Read Per Million unit, RPM)

organism: Caulobacter vibrioides

growth_protocol: Overnight cultures in PYE of C. crescentus CB15 ntrX::ntrX-HA were freshly restarted (starting O.D.660nm~0.05) in 80ml of PYE and incubated at 30°C under agitation.

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, the cell resuspension was incubated in the presence of Ready-Lyse lysozyme solution (Lucigen, #186002) for 10 min at 37 °C, according to the manufacturer's instructions. The lysate was sonicated (Bioruptor Pico) at 4 °C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3–0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4 °C. The volume of the lysate was then adjusted to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of Protein-A agarose (Roche) and 100 μg BSA. Five percent of the pre-cleared lysate was kept as total input sample (negative ChIP control sample). The rest of the pre-cleared lysate was then incubated overnight at 4°C with a monoclonal rabbit Anti-HA Tag antibody (Millipore, clone 114-2C-7; 1:400). The immuno-complexes were captured by incubation with Protein-A agarose beads (pre-saturated with BSA) during a 2 h incubation at 4°C and then, washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The immuno-complexes were eluted from the Protein-A beads with two times 250 μL elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like the total input sample, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 30 μl of DNAse/RNAse free water.
Immunoprecipitated chromatins were used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following the manufacturers’ instructions. A single-end run was performed on an Illumina Next-Generation DNA sequencing instruments (NextSeq High), 50 cycles were performed and yielded several million reads per sequenced samples.

treatment_protocol: Culture of exponentially growing C. crescentus CB15 ntrX::ntrX-HA (OD660 of 0.5, 80 ml of culture in PYE) was supplemented with 10 μM sodium phosphate buffer (pH 7.6) and then treated with formaldehyde (1% final concentration) at RT for 10 min to achieve crosslinking. Subsequently, the culture was incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellet was stored at -80 °C.

tag: chip antibody

value: Anti-HA (Merck Millipore, Clone114-2C-7)


title: RIB0020901_Pan_T_cells_act_72h_D4

city: Leipzig

first: Michael

last: Rade

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

data_processing:
Demultiplexing of Illumina raw files was performed with the Illumina bcl2fastq software v2.19.
Paired-end FASTQ reads were trimmed and filtered using AdaptorRemoval v2.3.1 with additional parameters to trim ambiguous bases (N) at 5’/3’ termini (–trimns), remove low-quality bases (–trimqualities, –minquality 20) and keep reads with a minimum read length of 30bp (–minlength 30).
Trimmed reads were mapped to the human reference genome version GRCh38/hg38 by HISAT2 v2.1.0 by specifying a reverse stranded library.
Gene level quantification for the human reference gene annotation GENCODE (release 29 GRCh38.p12) was obtained by using HTSeq v0.11.2 with following parameters: –mode intersection-strict, –stranded reverse and –type exon
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Comma-delimited text file with Counts Per Million (CPM) for each sample with the corresponsing Ensembl gene IDs.
Supplementary_files_format_and_content: Comma-delimited text file with raw gene counts for each sample with the corresponsing Ensembl gene IDs.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pan T-cells after activation, 72h

growth_protocol: Buffy coats were obtained from the Springe Blutspendedienst and were kept at 4 °C untill PBMC isolation. PBMCs were isolated by density centrifugation. The cell count and viability was determined with a hemocytometer and trypan blue staining. CD14+ monocytes, CD19+ B-cells and CD56+ natural killer cells were depleted using CD14, CD19 and CD56 magnetic cell sorting (MACS) beads (Miltenyi) following the manufactures instruction. The flow through was kept for CD2+ T-cell isolation. Therefore 1x10^7 cells were resuspended  and CD2 microbeads were added for 15 min at 4 °C After centrifugation (10 min, 300 xg, 4 °C) and resuspension of the cells in MACS-buffer. LS columns (Miltenyi) were placed into a magnet and cells were loaded onto the column through a pre-seperation filter (Miltenyi). The cell count was determined by trypan blue staining using a hemocytometer. Quality of the CD2+ isolation was confirmed by fluorescence-activated cell sorting (FACS).Isolated pan T cells (0.5-1×10^6) were incubated with 2.5 μL human TruStain FcXTM-block for 10 min at 4 °C. Viable cells were stained with Zombie NIRTM for 15 min at RT. Afterwards, cells were stained with CD3-FITC, CD45-AF700, CD-BV510, CD4-PacificBlue, Cd45RO-PE/Cy7, CD45RA-APC, CD14PerpCy/Cy5 (BioLegend, San Diego, USA) or respective isotype controls for 30 min on ice. Zombie NIRTM was used as a viability marker due to manufactures instructions. Samples were washed with 2 mL FACS buffer (PBS supplemented with 0.25% bovine serum albumin and 2 mM ethylenediaminetetraaceticacid (EDTA)). After centrifugation at 350 xg for 10 min, cells were resuspended. Viable leukocytes were discriminated from cell debris by forward (FSC) and sideward scatter (SSC) properties as well as CD45+, Zombie NIR+ cells Cells were separated by size in FS (Forward Scatter) and by granularity in SS (Sidewards Scatter). Subsequently, duplicates of singular cells were eliminated via the disproportion of height (PEAK) and width (TOF). The singular leukocytes negative for the dead dye ZombieNIR were further differentiated into monocytes (CD14) and CD3 T cells. NK cells and B cells were identified on CD3- cells using CD56 and CD19. CD3+ cells were further differentiated into T helper CD4+ and cytotoxic CD8+ cells. Naive T-cells were discriminated as CD45RA+ cells and memory T-cells as CD45RO+ cells.

extract_protocol:
For RNA sequencing, up to 0.5x10^6 treated or untreated T-cells per sample were collected. The cell pellets were re-suspended in Qiazol and stored at –80°C. RNA was extracted according to the miRNeasy mini protocol (Qiagen). After two steps of DNase-digestion (TURBO DNA free Kit, Ambion), extracted RNA was quantified using a Qubit RNA-Kit and the DeNovix instrument (Biozym). RNA quality was analyzed on a Bioanalyzer 2100 instrument (Agilent Technologies). For subsequent RNA-sequencing analyses, 150 ng of total RNA per sample were used.
Library preparation was conducted using Truseq-Stranded total RNA Sample Prep kit (Illumina, Inc, San Diego, CA) according to the manufacturers’ protocol. Molarity of each library was calculated and equal amounts were pooled and used for sequencing (12 pM). Sequencing was performed with 2 × 126-bp paired-end reads using HiSeq SBS Kit v4 chemistry on a HiSeq 2500 instrument (Illumina). Three flowcell à 8 lanes were sequenced with all 44-pooled libraries each.

treatment_protocol: 2x10^5 Pan T-cells were seeded in a 96 U-well plate with quadruplicates per condition. 2x10^5 Dynabeads human T-Activator CD3/CD28 (Gibco, 11132D) per sample were washed with PIB and were then resuspended in T cell medium (CG-DC-medium supplemented with 5% human AB serum and 1 % penicillin/streptomycin). 2x105 CD3/CD28 beads were added to activate T-cells and wells were filled up to 200 μL total volume. Unstimulated T-cells were used as controls. T-cells were harvested at different time points (0h, 6h, 12h, 24h, 48h, 72h). Therefore, unactivated and activated T-cells were collected and centrifuged (10 min, 300 xg, room temperature). 700 μL Trizol were added and sampels were stored at - 80 °C till RNA isolation.

value: PBMCs

tag: biological replicate

tag: time point

tag: activation

value: Anti-CD3/CD28 activation


title: siRNA-2_48H


title: siRNA-1_48H


title: MB53


title: 10_day, scRNAseq (spatial)

city: Shanghai

first: Ruifeng

last: Yang

address: Zhi Zao Ju Road

department: Molecular Diagnostics & Endocrinology

institute: Shanghai Ninth People's Hospital

description: 10x Genomics

data_processing:
Raw fastq files was processed using the Space Ranger (V1.2.1) and Seurat (V3.2.2) was used to process the Space Ranger output files. For the gene-spot matrixes generated by Space Ranger, some routine statistical analyses were performed first, including calculating the number of the detected UMIs and genes in each spot. on this basis, the spots with extremely low UMIs or genes were removed, and mitochondrial and ribosomal genes were filtered. According to morphological staining, we excluded non-thyroid area spots. This QC generated data sets containing 454 spots.
After QC, we used the R package harmony (v1.0) to integrate the expression data of the two mice thyroid tissues and used the Seurat package (v3.1.5) to perform the basic downstream analysis and visualization. In detail, UMI counts in each spot were normalized by the total transcript count and then scaled by the median number transcript count across all spots. Then we identified 2000 highly variable genes according to their expression means and variances for principal components analysis (PCA), which was performed to project the spots into a low-dimensional space (the first 20 principal components). Then, by setting the sample source as the batch factor and using the “RunHarmony” function, we iteratively corrected the spots’ low-dimensional PC representation to reduce the impact of individual difference. After this step, the corrected PC matrixes were used to perform unsupervised shared-nearest-neighbor (SNN)-based clustering and UMAP visualization analysis.
Assembly: mm10

source_name: Thyroid tissues

extract_protocol:
For ST transcriptional analysis, dissected thyroid cartilage area tissues from two mice were gently washed with cold phosphate-buffered saline (PBS) (Gibco, catalog no. 20012-043). Then the tissues were placed in OCT-filled mold and snap-frozen in isopentane and liquid nitrogen. Tissue blocks were stored at −80 °C for a maximum of 1 month before use. The Visium Spatial Gene Expression Slide (10 × Genomics, PN-1000185, Pleasanton, CA, USA) includes four capture areas (6.5 mm × 6.5 mm), each capture area has ~5000 gene expression spots, each spot with primers that include Illumina TruSeq Read 1 (partial read 1 sequencing primer), 16-nucleotide (nt) spatial barcode (all primers in a specific spot share the same spatial barcode), 12-nt UMI; 30-nt poly(dT) sequence (captures polyadenylated mRNA for cDNA synthesis)
After bright-field imaging, the thyroid ST slide was permeabilized at 37 °C for 24 minutes and washed with 100 μl of 0.1× SSC buffer. Then the on-slide reverse transcription (RT) reaction was performed at 53 °C for 2 hours. Second strand synthesis was subsequently performed on-slide for 15 minutes at 65 °C. Following second strand synthesis, thyroid sample was transferred to tubes containing tris-HCl (1 M; pH 7.0) for amplification and library construction. Library quality was assayed using 1 μl sample on a Bioanalyzer High Sensitivity chip (Agilent, catalog no. 50674626). 10× Genomics Visium libraries were prepared and sequenced on Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA) using a 28 bp + 120 bp paired-end sequencing mode. Sequencing data was processed using the Space Ranger pipeline v.1.0.0 (10 × Genomics). This generated data sets containing 1128 spots.

value: Thyroid tissues

value: Thyroid cells

value: 10 days old


title: A. fumigatus DtcsC, untreated, biol rep 1

value: Strain AfS35

value: mycelium


title: Total-Input_NtrX-HA_Caulobacter_crescentus_CB15_ntrX::ntrX-HA

tag: strain


title: DKO (Leu) 1 UB

value: Untreated, unbleached


title: A. fumigatus DtcsC, untreated, biol rep 4

value: No treatment

value: 0 h


title: PNA-4_48H


title: RIB0020937_Pan_T_cells_act_72h_D3


title: 30_day, scRNAseq

description: 10x Genomics

data_processing:
The gene-barcode matrix of UMI counts was then analyzed using Seurat (v3.6.3) 1 for quality control, normalization, dimensional reduction, batch effect removal, clustering, and visualization. The mean value of the mean reads per cell was 32,799, with a mean of 3,682 unique molecular identifiers (UMIs) per cell across all samples. We first filtered out low-quality cells that fitted any of the following criteria: proportion of mitochondrial gene counts > 10%, UMIs < 200, or UMIs > 10,000. Four samples were sequenced with a median of 9,375 cells per sample. After excluding low-quality cells and potential duplicates, we obtained 29,914 cells in total: 6,481 cells from 10 mice on postnatal day 5; 5,110 cells from 10 mice on postnatal day 10; 5996 cells from 10 mice on postnatal day 20; and 12,327 cells from 10 mice on postnatal day 30.
The count matrix was log-normalized, and the top 2,000 most variable genes were identified for dimensional reduction. The four datasets were integrated to remove batch effects with canonical correlation analysis, which identified cross-sample pairs of cells in a matched biological state as anchors and then used the anchors to correct technical differences between samples. The integrated matrix was then scaled, and we selected the top 30 principal components, based on the elbow plot heuristic as recommended by Seurat (v3.1.4), to get the UMAP plot. The FindNeighbors() and FindClusters() functions in Seurat were used for cell clustering. Meanwhile, shared nearest neighbor graph-based clustering was performed on the PCA-reduced data to identify the cell clusters. The resolution was set to 0.9, to obtain the major cell types of thyroid tissues. The cell identity of each cluster was determined with SingleR (v1.0.6) package 2 and then refined based on the expression of canonical marker genes.
Assembly: mm10

extract_protocol:
Thyroid tissues dissected from postnatal days 5, 10, 20, and 30 C57 mice were washed twice in 1 × PBS (Gibco) and cut into 1 mm3 pieces. Tissue pieces were then enzymatically digested with 3 mL digestion medium containing 5 mg/mL collagenase I/II, 0.2 u/mL dispase (Gibco), and 0.1 mg/mL DNAase. These samples were subsequently incubated at 37°C for 30 min in a water bath shaker, and the suspended cells were washed with 20% fetal bovine serum (FBS) in Dulbecco’s modified Eagle’s medium (DMEM), filtered through a 40 µm Cell-Strainer nylon mesh (BD), and centrifuged at 700 × g for 10 min. After washing with MACS buffer, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, Bielefeld, Germany), and the samples with cell viability > 90%, as assessed by trypan blue staining, were passed for initial quality control.
Sample libraries were prepared according to the Chromium Single Cell 3' Library and Gel Bead Kit instructions (v2-v3) and were sequenced on an Illumina NovaSeq 6000 System. The gene-barcode matrices were generated using CellRanger’s (v2-4) recommended pipeline, which aligned the droplet-based sequencing data against the mouse mm10 reference genome and counted the UMIs for each cell. The output was a count matrix containing all UMI counts for each droplet. Sequence alignment and transcript counts were performed using the CellRanger software.

value: 30 days old


title: MB52

data_processing:
The processing of myoblast Infinium Human MethylationEPIC data and all statistical analysis was conducted in R (v3.4.2).
Average Beta or normalized (provide the normalization method) Average Beta

extract_protocol: Genomic DNA (gDNA) was extracted from actively proliferating myoblasts using the GenEluteTM Mammalian Genomic DNA miniprep Kit (Merck) following manufacturer’s instructions.

value: Male


title: RIB0020916_Pan_T_cells_ctr_72h_D4

source_name: Pan T-cells without any treatments, 72h

value: Not activated


title: RIB0020919_Pan_T_cells_ctr_72h_D3


title: PNA-3_48H

value: Bone marrow

value: DLBCL


title: MB168

value: Female


title: WT-1 UB


title: MB51


title: MB54


title: RIB0020940_Pan_T_cells_ctr_72h_D2


title: MB49


title: RIB0020908_Pan_T_cells_act_72h_D2


title: 10_day, scRNAseq

description: 10x Genomics


title: 5_day, scRNAseq

description: 10x Genomics

value: 5 days old


title: RIB0020655_Pan_T_cells_act_72h_D1

value: PBMCs


title: MB127


title: PNA-2_48H

value: cmyc knockdown


title: PNA-1_48H


title: CD62L+ Tfh, ATAC-seq

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Raw ATAC-seq reads were trimmed and ﬁltered for quality control using Trim Galore v0.4.4 with parameters ‘-q 10 –length 30 –strin- gency 5 0 .
Clean paired-end reads were ﬁrst mapped to mouse geneme mm10 using Bowtie2 v2.2.9 with –x2000.
Non-uniquely mapping reads and reads that aligned to the mitochondrial genome were ﬁltered by Samtools.
PCR duplicates were removed with picard MarkDuplicates. Only concordantly mapped reads were used for further analyzing.
Peaks were determined by MACS2 with parameters ‘–nomodel–keep-dup all -q 0.01-shift 100-extsize 200 -call-summits -g mm’.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Draining lymph nodes

extract_protocol: The sample were prepared using Vazyme TruePrep DNA Library Prep Kit V2

value: Draining lymph nodes

tag: model

value: KLH immunization

value: day 8 post infection

value: CD62L+ Tfh


title: RIB0020627_Pan_T_cells_ctr_72h_D1


title: MB47

city: Southampton

first: Matthew

last: Hewitt

address: Institute of developmental sciences, 216 Tremona Road

institute: University of Southampton


title: CT-5_48H

value: WT


title: RIB0020967_Pan_T_cells_act_48h_D4

source_name: Pan T-cells after activation, 48h

value: Anti-CD3/CD28 activation


title: PD1+ Tfh, ATAC-seq

value: PD1+ Tfh


title: RIB0020913_Pan_T_cells_ctr_48h_D4

source_name: Pan T-cells without any treatments, 48h


title: CT-4_48H


title: MB46


title: non-Tfh, bulkRNA-seq

data_processing:
Clean reads were aligned to mm10 by bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 2fold change and fdr adjusted p-value 0.05
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include gene symbol and gene expression (or read count) for each sample

extract_protocol:
total RNA were extracted using RNeasy Plus Mini Kit (Qiagen, Cat No. 74134)
Library were constructed using SMARTer® Ultra® Low Input RNA for Illumina® Sequencing kit (Clontech Laboratories, Cat No. 010616)

value: day 8 post immunization

value: non-Tfh


title: 20_day, scRNAseq

description: 10x Genomics

value: Thyroid tissues

value: Thyroid cells

value: 20 days old


title: CD62L+Tfh, bulkRNA-seq


title: CT-3_48H

value: Bone marrow

value: DLBCL


title: RIB0020965_Pan_T_cells_act_48h_D3


title: PD-1+ Tfh, bulkRNA-seq

value: PD-1+ Tfh


title: RIB0020941_Pan_T_cells_ctr_48h_D3

value: PBMCs

value: Not activated


title: MB44

value: Male


title: RIB0020978_Pan_T_cells_act_48h_D2


title: MB45


title: Tfr, scRNA-seq

data_processing:
The quality of libraries was determined by Agilent 2100 bioanalyzer and sequenced with Hiseq-PE150(Illumina).
To generate single cell feature counts, the clean data of each sample were mapped to mouse reference genome (mm10) by the command “cell ranger count” within cell ranger toolkit (version 3.0.0) provided by 10X genomics.
Then Seurat (version 3.2.2)was used to perform dimensional reduction and clustering analysis of single-cell data
Datasets from different models (KLH,Tfr,FLU,PP) were integrated together by using the FindIntegrationAnchors and IntegrateData function from Seurat
Python package Velocyto was used for RNA velocity analysis
Assembly: mm10

extract_protocol:
Tfh (CD4+CD44hiCXCR5+Bcl6-RFP+B220-Foxp3-GFP-) and Tfr (CD4+CD44hiCXCR5+Bcl6-RFP+B220-Foxp3-GFP+) cells were sorted from indicated tissues via flow cytometer sorter
10x Genomics Single Cell 3’ Library preparation

value: Draining lymph nodes

value: KLH immunization


title: CT-1_48H


title: PP, scRNA-seq

source_name: Payer's patches

value: Payer's patches

value: steady state


title: MB120

value: Female


title: RIB0020922_Pan_T_cells_ctr_48h_D2


title: PNA2-5_72H

value: cmyc knockdown


title: PNA2-4_72H


title: FLU, scRNA-seq

value: H1N1 PR8 infection


title: CT-2_48H

value: WT


title: MB119


title: RIB0032709_Pan_T_cells_act_48h_D1

value: Anti-CD3/CD28 activation


title: KLH, scRNA-seq


title: MB118


title: RIB0020657_Pan_T_cells_ctr_48h_D1


title: PNA2-3_72H


title: RIB0020917_Pan_T_cells_act_24h_D4

source_name: Pan T-cells after activation, 24h


title: PNA2-2_72H


title: CD8,scRNAseq

city: Dallas

first: Todd

last: Aguilera

state: TX

address: 2280 Inwood Rd

department: Molecular radiation biology

institute: UTSouthwestern- Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Hierarchical Data Formats HDF5 and matrix files

source_name: Py8119 tumor

extract_protocol:
Mice injected with VHHs phage display specific libraries for CD8 T cells, DC, and CD45 we also injected PBS as a negative control, and insertless phage as a positive control(three mice per group). After two hours tissues were mechanically minced and digested for 40 min with 100 U/ml Collagenase IV (Worthington), 10 mg/ml DNAse (Sigma Aldrich) and 10.5 mM Y-27632 (Sigma  Aldrich) in HBSS (Corning) and RPMI 1640 (Mediatech, Inc., Corning) complemented with 3 %  FetalClone II (HyClone). Immune cells were enriched using CD45 magnetic microbeads. Viability and cells count was measured by 0.4 % Trypan blue exclusion method. Cells were frozen in FBS + 10% DMSO. At the time of sequencing, thawed cells were counted using a TC20 automated cell counter (BioRad) and adjusted to 1000 cells/ul in 0.04 % BSA/PBS and 1 ml/sample were submitted to the Next Generation Sequencing Core.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Immune cells

value: Py8119 tumor

value: 6-12 weeks old


title: DC,scRNAseq

description: 10x Genomics

value: DC


title: MB116


title: MB42


title: MB115


title: Control-5_72H

value: Bone marrow

value: DLBCL


title: RIB0020923_Pan_T_cells_ctr_24h_D3

source_name: Pan T-cells without any treatments, 24h

value: PBMCs

value: Not activated


title: MB114


title: Control-4_72H


title: Control-3_72H


title: CD45, scRNAseq

description: 10x Genomics


title: PBS,scRNAseq

description: 10x Genomics

value: PBS


title: Insertless_phage, scRNAseq

description: 10x Genomics


title: MB113


title: RIB0020695_Pan_T_cells_ctr_24h_D2


title: MB33


title: HFHS + NAC, rep 2

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

institute: UNIL

data_processing:
reads where trimmed from adapter sequence using cutadapt (ersion: 3.5; options: --match-read-wildcards --overlap 8 --discard-untrimmed --minimum-length 30) and quality filtered using faion: 0.0.14; options: -Q33 -q 30 -p 90)
UMIs were extracted from each read with UMItools (options: extract --extract-method string --bc-pattern NNNNNNNNCCCCC --3prime --filter-cell-barcode –error-correct-cell).
Reads where size-selected for single ribosome (monosomes; size 26 to 35). To estimate rRNA and tRNA contamination, reads were mapped to human and mouse rRNA and mouse tRNA databases using bowtie2 (options: -p 2 -L 15 -k 20 --trim5 2). Reads that failed to map to these, where then mapped to the mouse transcript database (Ensembl database v. 100).
Assembly: Ensembl transcript v100
Supplementary files format and content: Samples SGA files: tab delimited file reporting transcript ID, sample type, position, strand and read counts of predicted ribosome A sites.
Supplementary files format and content: codonCount.dat: tab delimited file with the following columns: Gene ID, transcript ID, codon position, read counts for each sample
Library strategy: Ribo-seq

source_name: Liver

growth_protocol: Young male mice (aged 10-15 weeks) were maintained under standard housing conditions with 12:12 hour light:dark cycle in ventilated cages at room temperature with ad libitum access to food and water.

extract_protocol:
From RNase I-digested liver lysates, RNA was extracted and 2 μg of RNA were separated on a 15% urea-polyacrylamide gel. After size selection of ribosome footprints from the gel, RNA was extracted from the excised gel slices overnight at 4°C on a rotating wheel before precipitation in isopropanol during 3h at -20°C and recovery and solubilisation in water.
RNA 3’-end repair was carried out with 2 U/μl of T4 PNK (Lucigen) prior to a 2h adaptor ligation at 25°C using 1.5 μl of ligase mix (3.3 U/μL of T4 RNA Ligase 1 (NEB), 66.6 U/μl of T4 RNA Ligase 2 Deletion Mutant (Lucigen) and 13.3 U/μL of riboguard (Lucigen)) and 1 uL of a 20 μM 5’-adenylated DNA adaptor (containing sample barcode and a 8N unique molecular identifiers (UMIs)). Adaptor removal was carried out by treating individual libraries with 2.7 U/μl of 5’deadenylase (NEB) and 5.5 U/μL of RecJ exonuclease (Lucigen) for 1h at 30°C and 1h at 37°C. Using Zymo Clean & Concentrator columns, samples were purified and pooled. Ribosomal RNA was depleted according to siTools Biotech rRNA depletion kit specifications with minor variations: 4 μl of a custom-made riboPOOL was used to deplete rRNA and the clean-up step was done using Zymo Clean & Concentrator columns

treatment_protocol: Mice received either standard commercial rodent chow or high-fat-high-sucrose (HFHS) diet (Research Diets, #D12331) for 8 weeks, whereby fresh food pellets were provided to the mice once per week. For each of the two diet treatments, 3 mice received normal drinking water, and 3 mice received drinking water supplemented with 2 g/l N-acetylcysteine (NAC). The compound was added directly to the drinking water and the solution was refreshed 3x per week. After 8 weeks treatment, animals were sacrificed, livers extracted and snap-frozen.

value: Liver

value: male

tag: diet

value: High Fat High Sugar Diet

value: NAC


title: MB117

value: Female


title: PNA2-1_72H

value: cmyc knockdown

tag: time


title: Control-2_72H

value: WT


title: MB36

value: Male


title: Control-1_72H


title: RIB0020943_Pan_T_cells_ctr_24h_D4


title: RIB0020683_Pan_T_cells_act_24h_D1

value: Anti-CD3/CD28 activation


title: HFHS + NAC, rep 1


title: MB32


title: RIB0020934_Pan_T_cells_act_24h_D3


title: RIB0020684_Pan_T_cells_ctr_24h_D1


title: CHD MPRA in iPSC-CMs day 24 RNA-Rep-4

city: Jamaica Plain

first: Xiaoran

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

data_processing:
Cutadapt 2.5 was used to remove primer sequences within each read.
Sequence reads were mapped to library variants based on the barcode by a custom Python script.
Read counts were then normalized to sequencing depth (FPM).
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files include reads count values for each Sample.
Library strategy: Amplicon-seq

growth_protocol: iPSC-CMs were maintained in RPMI supplemented with B27 supplement in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Both DNA and RNA were extracted from transfected iPSC-CMs using Quick-DNA/RNA Miniprep Kit (Zymo #D7001). Purified genomic DNA and RNA were stored at -80C.
RNA was transcribed into cDNA with a specific primer using the PrimeScript™ RT reagent Kit with gDNA Eraser (Takara #RR047A). Amplicons containing 15 bp barcodes were amplified from gDNA and cDNA.

treatment_protocol: iPSC-CMs were transfected with the CHD lentiMPRA library at day 17 of iPSC-CM differentiation, and cells were collected 7 days later.

value: iPSC-derived cardiomyocytes

value: Transduced with lentiMPRA lentivirus


title: Chow + NAC, rep 3

value: Chow Diet


title: RIB0020650_Pan_T_cells_act_24h_D2


title: CHD MPRA in iPSC-CMs day 24 RNA-Rep-3


title: MB31


title: MB30


title: CHD MPRA in iPSC-CMs day 24 RNA-Rep-2


title: Chow + NAC, rep 2


title: RIB0020990_Pan_T_cells_ctr_12h_D4

source_name: Pan T-cells without any treatments, 12h


title: MB29


title: RIB0020959_Pan_T_cells_act_12h_D3

source_name: Pan T-cells after activation, 12h


title: CHD MPRA in iPSC-CMs day 24 RNA-Rep-1


title: MB27


title: Chow + NAC, rep 1


title: CHD MPRA in iPSC-CMs day 24 DNA-Rep-4


title: RIB0020960_Pan_T_cells_ctr_12h_D3


title: HFHS, rep 2


title: CHD MPRA in iPSC-CMs day 24 DNA-Rep-3


title: HFHS, rep 3


title: RIB0020649_Pan_T_cells_act_12h_D2


title: MB26


title: MB25


title: HFHS, rep 1


title: CT-6_48H

value: Bone marrow


title: RIB0020671_Pan_T_cells_ctr_12h_D2


title: RIB0020950_Pan_T_cells_act_12h_D4


title: Chow, rep 3


title: MB24


title: RIB0020699_Pan_T_cells_act_12h_D1


title: CHD MPRA in iPSC-CMs day 24 DNA-Rep-1


title: HFHS + NAC, rep 3


title: Mutagenesis MPRA in iPSC-CMs day 24 RNA-Rep-4

data_processing:
Cutadapt 2.5 was used to remove primer sequences within each read.
Sequence reads were mapped to library variants based on the barcode by a custom Python script.
Read counts were then normalized to sequencing depth (FPM).
Assembly: hg19
Supplementary files format and content: *.txt: Tab-delimited text files include reads count values for each Sample.
Library strategy: Amplicon-seq

treatment_protocol: iPSC-CMs were transfected with the mutagenesis lentiMPRA library at day 17 of iPSC-CM differentiation, and cells were collected 7 days later.


title: Chow, rep 2


title: MB23


title: Chow, rep 1


title: RIB0020700_Pan_T_cells_ctr_12h_D1


title: CHD MPRA in iPSC-CMs day 24 DNA-Rep-2


title: MB22


title: MB21


title: Mutagenesis MPRA in iPSC-CMs day 24 RNA-Rep-2


title: Mutagenesis MPRA in iPSC-CMs day 24 RNA-Rep-3


title: Multiplex_pancreas_organoids CMO

description: 10x Genomics

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v6.1.1)
cellranger mkfastq was used for fastq generation. Gene expression data was stored in the *GEX* files and Cell multiplexing oligo data was stored in the *CMO* files.
cellranger multi was used to separate samples based on their cell multiplexing oligo (CMO), align reads to the 10X pre-build mouse reference genome (mm10) and extract gene expression UMI counts matrix.
Assembly: mm10
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.
Supplementary files format and content: Each cell barcode contains a prefix that indicates which sample it is from. 'D01' --> WT; 'D02' --> KC; 'D03' --> KPC; 'D04' --> KSC; 'D05' --> KPSC; 'D06' --> WT-P; 'D07' --> KC-P; 'D08' --> KPC-P; 'D09' --> KSC-P; 'D10' --> KPSC-P

source_name: Pancreas

extract_protocol:
Cultured organoids were collected from 24 well plates and dissociated with Accutase to obtain single cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Pancreas

value: Pancreas Organoids

value: wild type

value: treated with or without perhexiline


title: RIB0020936_Pan_T_cells_ctr_6h_D4

source_name: Pan T-cells without any treatments, 6h

value: PBMCs

value: Not activated


title: Mutagenesis MPRA in iPSC-CMs day 24 RNA-Rep-1


title: Multiplex_pancreas_organoids GEX

description: 10x Genomics


title: MB19


title: RIB0020935_Pan_T_cells_act_6h_D4

source_name: Pan T-cells after activation, 6h


title: MB18

source_name: Myoblast gDNA isolated and cultured from vastus lateralis muscle tissue


title: RIB0020930_Pan_T_cells_act_6h_D3


title: lentiMPRA in iPSC-CMs day24 RNA-Rep6

data_processing:
Cutadapt 2.5 was used to remove primer sequences within each read.
MPRA pair-end reads were aligned to hg19 using Bowtie2 2.3.4.3 (--end-to-end) with default parameters.
A custom Python script was used to determine DNA and RNA read counts for each enhancer.
Read counts were then normalized to sequencing depth (FPM).
Assembly: hg19
Supplementary files format and content: *.txt: Tab-delimited text files include reads count values for each Sample.
Library strategy: Amplicon-seq

extract_protocol:
Both DNA and RNA were extracted from transfected iPSC-CMs using Quick-DNA/RNA Miniprep Kit (Zymo #D7001). Purified genomic DNA and RNA were stored at -80C.
RNA was transcribed into cDNA with a specific primer using the PrimeScript™ RT reagent Kit with gDNA Eraser (Takara #RR047A). Amplicons containing 400 bp tested regions were amplified from gDNA and cDNA.

treatment_protocol: iPSC-CMs were transfected with the lentiMPRA library at day 10 or 17 of iPSC-CM differentiation, and cells were collected 7 days later.

value: Transduced with lentiMPRA lentivirus at day24


title: Mutagenesis MPRA in iPSC-CMs day 24 DNA-Rep-4


title: lentiMPRA in iPSC-CMs day24 RNA-Rep5


title: RIB0020918_Pan_T_cells_ctr_6h_D3


title: Mutagenesis MPRA in iPSC-CMs day 24 DNA-Rep-3


title: MB17


title: RIB0020548_Pan_T_cells_ctr_6h_D2


title: RIB0020648_Pan_T_cells_act_6h_D2


title: Mutagenesis MPRA in iPSC-CMs day 24 DNA-Rep-2


title: MB16


title: RIB0020694_Pan_T_cells_act_6h_D1


title: lentiMPRA in iPSC-CMs day24 RNA-Rep4


title: MB15


title: lentiMPRA in iPSC-CMs day24 RNA-Rep3


title: MB134


title: Mutagenesis MPRA in iPSC-CMs day 24 DNA-Rep-1


title: Hashed PacBio scBCR library 1

source_name: Peripheral Blood

value: Peripheral Blood

value: B-Lymphocyte


title: MB9

value: Female


title: lentiMPRA in iPSC-CMs day24 RNA-Rep2

value: WT


title: Hashed PacBio scBCR library 2


title: SK-HEP1_siSFPQ_T

city: Hangzhou

first: Mu

last: Xiao

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Sequenced reads were trimmed to 50bp and mapped to the human genome (hg19) using Tophat v2.1.1.
Mapped reads (~95% of total reads) were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) with Cufflinks v2.2.1.
Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments)
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited text file includes RPKM values for each samples

growth_protocol: HCC cells were cultured in DMEM medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.  VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (NR601-01) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with TGF-b (2 ng/ml) for 24 hours

value: HCC

value: SFPQ KD

value: withTGF-betatreatment


title: lentiMPRA in iPSC-CMs day24 DNA-Rep5

last: Zhang

value: iPSC-derived cardiomyocytes


title: MB11


title: RIB0020659_Pan_T_cells_ctr_6h_D1


title: SK-HEP1_siCTL_T

value: wt


title: lentiMPRA in iPSC-CMs day24 RNA-Rep1


title: MB5


title: RIB0020932_Pan_T_cells_0h_D4

source_name: Pan T-cells without any treatments, 0h


title: lentiMPRA in iPSC-CMs day24 DNA-Rep6


title: MB6


title: SK-HEP1_siSFPQ

value: withoutTGF-betatreatment


title: RIB0020696_Pan_T_cells_0h_D2


title: RIB0020665_Pan_T_cells_0h_D1


title: MB4


title: RIB0020971_Pan_T_cells_0h_D3


title: SK-HEP1_siCTL


title: lentiMPRA in iPSC-CMs day24 DNA-Rep4


title: MB3


title: HLE_siSFPQ_T

source_name: HLE

value: HLE


title: MB151


title: HLE_siSFPQ


title: parental strain no iron repl 2

city: Durham

first: Amy

middle: K

last: Schmid

address: 125 Science Dr.

department: Biology

institute: Duke University

description: ∆pyrE

data_processing:
50bp paired reads were quality checked using FastQC, adapter sequences trimmed using Trim Galore and Cutadapt.
Result sequences were aligned to the Haloferax volcanii DS2 genome (RefSeq GCF_000025685.1) using Bowtie2.
BAM files were generated using samtools, they were inputs to generate count files using HTSeq (count files associated with each sample are included in this GEO dataset)
Count files were input into DeSeq2 to generate normalised counts, exclude outlier samples, and generate lists of differentially expressed genes in pairwise comparisons.
Assembly: GCF_000025685.1
Supplementary files format and content: tab-delimited text file with raw counts for each gene

organism: Haloferax volcanii

source_name: archaeal cells

growth_protocol: Triplicate cultures of strains ∆pyrE (control strain) and  ∆troR (TF knockout strain) were grown in rich media overnight and then washed and resuspended in minimal media  supplemented with iron until stationary phase; finally,  cells were subcultured in minimal media with or without iron  until  mid-log phase (OD600 ~0.4). Cells were then pelleted, freezed with N2 and processed.

extract_protocol:
RNA was extracted using the Agilent Kit as per the manufacturer's protocol, quantified by bioanalyzer and checked for quality by PCR to ensure that it was not contaminated by gDNA. rRNA removal using RiboZero
Libraries were constructed using the KAPA Hyper Prep kit and Illumina TruSeq adapters according to manufactuer's instructions. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent). Samples were pooled and run in a single lane on an Illumina HiSeq 4000 (Duke Sequencing and Genomics Technologies core).

treatment_protocol: Cells were grown in Minimal Media (PR) with 100 microM Fe2SO4 or PR treated with iron chelator BPS and without iron addition.

value: archaeal cell

value: {delta}pyrE

tag: growth phase

value: mid-log

tag: condition

value: iron chelated


title: parental strain no iron repl 1

description: ∆pyrE

tag: cell type


title: MB1


title: troR knockout repl 3

description: ∆pyrE ∆troR

value: {delta}pyrE {delta}troR

value: 100 mM Fe2SO4


title: HLE_siCTL_T


title: lentiMPRA in iPSC-CMs day24 DNA-Rep2

value: Transduced with lentiMPRA lentivirus at day24


title: lentiMPRA in iPSC-CMs day17 RNA-Rep5

value: Transduced with lentiMPRA lentivirus at day17


title: HLE_siCTL


title: HepG2_siSFPQ_T


title: lung adenocarcinoma cell line 2

city: Hohhot

first: Ruihua

address: No.24 Zhaogun Road

institute: Inner Mongolia University

data_processing:
libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts
then transformed into clean reads and mapped to the reference genome sequence using Hisat2 tools soft.
Homo_sapiens.GRCh38_release95.genome was used to as a control to map the data
HISAT2 was used to compare the effective data of the sample to the reference genome, and the Mapping information was collected
The StringTie Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts.
DESeq2 was provided to analyze differential gene expression of each group.

source_name: Human lung

growth_protocol: The cell line HBE was cultured in RPMI-1640 medium, the A549 cell line in DMEM medium, both media were supplemented with 10% fetal bovine serum, streptomycin (100 mg/mL), and penicillin (100 µg/mL). The cells were maintained at 5% CO2 and 37 ℃.

extract_protocol:
total RNAs were extracted from HBE and A549 cells using RNAprep Pure Plant Kit (Tiangen, Beijing, China) and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Libraries were prepared by Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.). The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system

tag: tissue

value: Human lung

value: lung adenocarcinoma cell


title: lung adenocarcinoma cell line 3


title: lentiMPRA in iPSC-CMs day17 RNA-Rep4

tag: genotype

value: WT


title: troR knockout repl 1

description: ∆pyrE ∆troR


title: lentiMPRA in iPSC-CMs day17 RNA-Rep3

tag: treatment


title: troR knockout repl 2

description: ∆pyrE ∆troR


title: lentiMPRA in iPSC-CMs day24 DNA-Rep3


title: lentiMPRA in iPSC-CMs day17 RNA-Rep2


title: normal lung epithelium cell line 3

value: HEB

value: normal lung epithelium cell


title: parental strain repl 3

description: ∆pyrE


title: lung adenocarcinoma cell line 1


title: HepG2_siSFPQ

value: HCC

value: SFPQ KD


title: HepG2_siCTL_T

value: wt

value: withTGF-betatreatment


title: parental strain no iron repl 3

description: ∆pyrE

value: archaeal cell


title: parental strain repl 2

description: ∆pyrE

value: {delta}pyrE


title: lentiMPRA in iPSC-CMs day24 DNA-Rep1

value: iPSC-derived cardiomyocytes


title: lentiMPRA in iPSC-CMs day17 RNA-Rep1


title: lentiMPRA in iPSC-CMs day17 RNA-Rep6


title: normal lung epithelium cell line 2


title: parental strain repl 1

description: ∆pyrE

value: mid-log


title: HepG2_siCTL

value: withoutTGF-betatreatment


title: normal lung epithelium cell line 1


title: Huh7_siSFPQ_T


title: lentiMPRA in iPSC-CMs day17 DNA-Rep5


title: lentiMPRA in iPSC-CMs day17 DNA-Rep6


title: MOLM13 OE RBM5 cDNA targeted cells rep3 [MOLM13-R5_OE_3]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

description:
RNA.UNSTRANDED_RSEM_gene_TPM.tsv.gz
RNA.UNSTRANDED_RSEM_gene_counts.tsv.gz

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore.
Paired-end reads were mapped by STAR(v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM".
Read duplication was marked with MarkDuplicates from GATK (v4.1.2.0).
RSEM was used to quantify read counts per gene.
Assembly: hg19 (GRCh37.p13)
Supplementary files format and content: gene-based raw counts as well as FPKM and TPM normalized txt files

source_name: human AML MOLM13

growth_protocol: Leukemia lines MOLM-13 cells were maintained in RPMI-1640 medium (CORNING, 10-040-CV) containing 10% fetal bovine serum (FBS) (HyClone, 03.N16001DC).

extract_protocol:
RNA samples of 3 biological replicates were extracted from cultured cells, using TRIZOL (Ambion by Life technologies, 343911), following the manufacturer’s instructions.
About 200 ng total RNA was treated using Kapa rRNA depletion reagents to remove ribosomal RNA, then converted into cDNA libraries using Kapa RNA HyperPrep Kit with RiboErase (HMR). After end repair, dA-tailing, and adapter ligation, each cDNA library was purified and enriched by 11 cycles of PCR amplification. All RNA-seq libraries underwent 101-cycle paired-end sequencing on the Illumina Novaseq system.
Quality control filtering and adapter trimming of fastq files was performed with trim_galore. Paired-end reads were mapped by STAR(v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM". Read duplication was marked with MarkDuplicates from GATK (v4.1.2.0). RSEM was used to quantify read counts per gene. Differentially expressed genes were identified using the generated count data described above and DESeq2 (version 1.14.0).

value: human AML MOLM13

value: MLL-r leukemia cell line

value: RBM5 OE

value: oe

value: no treatment


title: troR_IP_2

description: ∆pyrE+TroR::HA

data_processing:
Gzipped FASTQ files were assessed for quality using FastQC and adapter sequences trimmed using Cutadapt/Trim Galore
Trimmed fastq files were aligned to the Haloferax volcanii DS2 genome (GCF_000025685.1) using Bowtie2. Samtools was used to generate and sort BAM files. Sorted BAM files were used for further analysis.
Peak-calling was done on sorted BAM files using Mosaics package within R (fragment size 200)
WIG files were generated using the samtools mpileup command. Per-base count files were generated using bedtools genomecov
Assembly: GCF_000025685.1
Supplementary files format and content: WIG file

growth_protocol: Strains (H26, H176 and H177)  were struck from freezer in YP18%uracil+ plates until individual colonies were visible (~4 days); Independent colonies were used to start  cultures  in 10 mL YPC18+uracil. Precultures were grown overnight at 42C with 250 rpm shaking, then collected at 6000 rpm for 2 min and washed twice with minimal media PR. Pellets were resuspended in PR+ overnight until saturation and then resuspended again in PR+ OD=0.01 until they reach  mid-log phase (OD = 0.4-0.6). Cell pellets were harvested, crosslinked with formaledhyde, and frozen for immunoprecipitation

extract_protocol:
Samples processed using Wilbanks et al. (2012)  protocol;  anti-HA polyclonal antibody (Abcam #ab9110) to immunoprecipitate cross-linked fragments.
Libraries were constructed by the Center for Genomic and Computational Biology at Duke University (Durham, NC) using KAPA Hyper Prep kit and Illumina TruSeq adapters, and the 50 bp, single-ended libraries were sequenced on an Illumina HiSeq 4000

treatment_protocol: minimal media supplemented with 100 microM Fe2SO4

value: 100 mM Fe2SO4 (Fe+)

value: Abcam #ab9110

tag: epitope tag

value: HA

tag: fraction

value: genomic DNA IP


title: troR_IP_4

description: ∆pyrE+TroR::HA


title: lentiMPRA in iPSC-CMs day17 DNA-Rep4

tag: cell line

value: WT

value: Transduced with lentiMPRA lentivirus at day17


title: troR_IP_1

description: ∆pyrE+TroR::HA

tag: chip antibody


title: lentiMPRA in iPSC-CMs day17 DNA-Rep3


title: Huh1_siSFPQ_T

value: HCC

value: SFPQ KD

value: withTGF-betatreatment


title: sirR_IP_2

description: ∆pyrE+SirR::HA

value: archaeal cell


title: lentiMPRA in iPSC-CMs day17 DNA-Rep2

value: iPSC-derived cardiomyocytes


title: Huh1_siSFPQ

value: withoutTGF-betatreatment


title: MOLM13 OE RBM5 cDNA targeted cells rep2 [MOLM13-R5_OE_2]

value: human AML MOLM13


title: MOLM13 OE RBM5 cDNA targeted cells rep1 [MOLM13-R5_OE_1]

value: MLL-r leukemia cell line


title: pyrE_IP

description: ∆pyrE (parental, no-tag control)

value: {delta}pyrE (parental, no-tag control)

value: mid-log


title: MOLM13 sgRBM5 targeted cells rep3 [MOLM13-R5_KO_3]

value: RBM5 KO

value: ko

value: no treatment


title: MOLM13 sgRBM5 targeted cells rep2 [MOLM13-R5_KO_2]


title: WTC-Cas9 iPSC-CMs day17 Rep-6

description:
WTC-Cas9-CM-6
WT-6

data_processing:
RNA-seq mapping and quantitation were done using STAR v. 2.6.147 with a hg38 STAR index.
The mapped reads were further analyzed by HTSeq-count v.0.11.2 and annotated using a RefSeq database.
The reads count were normalized by DEseq2.
Assembly: hg38
Supplementary files format and content: *.readscount.txt: Tab-delimited text files include raw counts.
Supplementary files format and content: WTC_CM_normalized_readscount.txt: Tab-delimited text file includes RPKM values for each Sample.

extract_protocol:
iPSC-CMs were lysed in TRIzol reagent (Invitrogen) and total RNA were extracted according to the instructions. Purified RNA was kept at -80C prior to sequencing.
RNA samples were analyzed by TapeStation (Agilent) and libraries were generated and sequenced by Genewiz. RNA was processed with poly(A) selection for full length transcripts. Libraries were sequenced on an Illumina HiSeq platform using the 2x150bp configuration with single index.

value: wildtype

value: cardiomyocyte differentiation


title: Huh7_siSFPQ


title: Huh1_siCTL_T

value: wt


title: MOLM13 sgRBM5 targeted cells rep1 [MOLM13-R5_KO_1]


title: WTC-Cas9 iPSC-CMs day17 Rep-5

description:
WTC-Cas9-CM-5
WT-5


title: MOLM13 sgNT targeted cells rep3 [MOLM13-NT_3]

value: control


title: Huh1_siCTL

value: HCC


title: troR_WCE_4

description: ∆pyrE+TroR::HA

value: 100 mM Fe2SO4 (Fe+)

value: HA

value: genomic DNA WCE


title: WTC-Cas9 iPSC-CMs day17 Rep-4

description:
WTC-Cas9-CM-4
WT-4

value: iPSC-derived cardiomyocytes


title: Huh7_siCTL_T

value: withTGF-betatreatment


title: Hep3b_siSFPQ_T

value: SFPQ KD


title: Huh7_siCTL

value: withoutTGF-betatreatment


title: MOLM13 sgNT targeted cells rep2 [MOLM13-NT_2]

value: human AML MOLM13

value: MLL-r leukemia cell line


title: troR_WCE_1

description: ∆pyrE+TroR::HA

value: archaeal cell

value: mid-log


title: Hep3b_siSFPQ


title: WTC-Cas9 iPSC-CMs day17 Rep-3

description:
WTC-Cas9-CM-3
WT-3


title: lentiMPRA in iPSC-CMs day17 DNA-Rep1

value: WT

value: Transduced with lentiMPRA lentivirus at day17


title: MOLM13 sgNT targeted cells rep1 [MOLM13-NT_1]

value: no treatment


title: sirR_IP_1

description: ∆pyrE+SirR::HA

value: Abcam #ab9110

value: genomic DNA IP


title: WTC-Cas9 iPSC-CMs day17 Rep-2

description:
WTC-Cas9-CM-2
WT-2

value: wildtype

value: cardiomyocyte differentiation


title: Hep3b_siCTL_T

value: HCC

value: wt


title: sirR_WCE_2

description: ∆pyrE+SirR::HA

value: 100 mM Fe2SO4 (Fe+)

value: HA

value: genomic DNA WCE


title: sirR_WCE_1

description: ∆pyrE+SirR::HA


title: PLC_Hyp-NFX1

city: Hefei

first: Ronghui

last: Yan

state: Anhui

address: Huangshan road 443

institute: University of Science and Technology of China

data_processing:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 v.2.1.0
Transcripts were assembled and gene expression analysis was performed by Cufflinks V2.2.1
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

growth_protocol: PLC/PRF/5 cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin–streptomycin (Hyclone)

extract_protocol:
Total RNA was extracted using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hypoxia

value: Hypoxia


title: PLC_Hyp-EV

value: EV


title: Hep3b_siCTL

value: withoutTGF-betatreatment


title: WTC-Cas9 iPSC-CMs day17 Rep-1

description:
WTC-Cas9-CM-1
WT-1

value: iPSC-derived cardiomyocytes


title: troR_WCE_2

description: ∆pyrE+TroR::HA

value: archaeal cell

value: mid-log


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-P24

status: Public on Nov 15 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: cj1700_1.1 (calJac4), annotation: GCA_009663435.2
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

organism: Callithrix jacchus

extract_protocol:
Motor cortex of brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously22. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

tag: brain region

value: Motor cortex

tag: gender

value: M


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-P23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-P12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-N23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-O11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-P11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-N24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-O24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-O12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-N12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-N11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-M24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-M11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-M23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-L24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-M12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-L23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-L12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-L11


title: pyrE_WCE

description: ∆pyrE (parental, no-tag control)

value: {delta}pyrE (parental, no-tag control)


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-K24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-K11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-O23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-J23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-J24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-K23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-J12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-I24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-I12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-I23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-I11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-H12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-H23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-G12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-G24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-H11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-G23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-G11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-K12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-F24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-E24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-J11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-F11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-E23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-D24


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-E11


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-D12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-D23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-C12


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-C23


title: CEMBA3C_MarmosetM1_R2_P8-6-E22-D11