title: GFP+

city: Lincoln

first: Charles

last: Wood

state: Nebraska

department: School of Biological Sciences

institute: University of Nebraska-Lincoln

data_processing:
Quality control of the reads was carried out using FastQC version 0.1 and Trimmomatic tools version 0.33 to filter out low-quality, adapters, and overrepresenting reads with the following config: (PE -phred33 ILLUMINACLIP:Adapters.fa:2:20:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
Qualified reads were aligned against the hg19 genome using the TopHat tool version 2.1. The aligned reads were used to calculate the expression levels as FPKM (fragments per kilobase of exon per million reads) values using the Cufflinks tool version 2.2.
Differentially expressed genes, and fold changes among the phenotypically segregated populations were obtained using the CuffDiff tool and FDR < 0.05.
Unmapped reads to hg19 were converted to paired-end reads in fastq files using SAMtools version 1.3, and aligned against the KSHV genome (GenBank accession no. NC_009333.1) using TopHat version 2.1 for viral analysis.
Using the Cufflinks tool version 2.2, the expression levels of KSHV genes for each sample is obtained based on the the mapped reads to the KSHV genome.
Genome_build: hg19, and NC_009333.1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample aligned against hg19 and KSHV genomes.
Supplementary_files_format_and_content: Tab-delimited text file contanis the log2 foldchanges (differential gene expressions) of infected samples compared to the control sample.

source_name: KSHV latent infection

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 50mg/ml streptomycin and 50U of penicillin and 6 ug/ml puromycin. The cells were maintained at 37°C with 5% CO2.

extract_protocol:
RNA extractions from recombinant rKSHV.219 infected and non-infected SH-SY5Y cells were carried out according to the miRNeasy Mini Handbook (Qiagen).
The samples’s RNA (5ug) were purified using Agencourt AMPure XP SPRI beads (Beckman Coulter, Brea, CA, USA) to remove chemical contaminants and short RNAs less than 200 nt in length, and then further reverse transcribed to double stranded cDNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Thermo Fisher). Random hexamers (New England BioLabs, Ipschwich, MA, USA) were used for priming the first strand synthesis reaction.Samples were prepared for RNA-seq using Illumina compatible Epicentre Nextera™ technology. After limited cycle PCR the RNA-seq libraries were size selected (350–700 bp fragments) in 2% agarose gel followed by purification withthe QIAquick gel extraction kit (Qiagen).

treatment_protocol: SH-SY5Y cells at 1×105 / ml were seeded in a volume of 1 ml in a 12-well plate. The cells were infected with rKSHV.219 at a multiplicity of infection (MOI) of 0.5 on the following day. The culture plate was centrifuged at 300 × g for 20 min at 25°C to promote viral contact with target cells. Infected cultures were maintained for 2 weeks and passaged to maintain the approximately 70-80% confluent growth. Infection phenotype was monitored by fluorescence microscopy (Nikon Eclipse TE300) for GFP/RFP expression. Fluorescent microscopic images were digitally acquired using the TE300 with NIS-Elements-inverted software (Nikon, USA).

value: bone marrow

value: neuroblastoma

value: KSHV infected GFP+ SH-SY5Y


title: RG+

status: Public on Apr 26 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: KSHV lytic infection

tag: cell line

tag: tissue

tag: cell type

tag: treatment

value: KSHV infected RFP+/GFP+ SH-SY5Y


title: PAG102_NonInf Malaria Before Infection mRNA Year2 Sample

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
raw reads were processed using Trimmomatic v0.36 to remove adapter sequences and low-quality bases (Phred quality score < 20).
 Filtered reads were then mapped to the human reference genome (Ensembl GRCh38 release-84) using STAR v2.5.0c.
Transcripts abundances were estimated as transcripts per million
Only genes with a minimum of 1 TPM in 10 samples per experimental condition were retained for downstream analyses
Genome_build: hg38

source_name: Blood

extract_protocol:
globin-mRNA depletion using the GlobinClear kit (Thermo Fisher)
KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems) and 100 bp paired-end sequencing using the TruSeq SBS Kit v3 - HS (Illumina)

tag: visit

value: Malaria Before Infection


title: INPUT-93T449-BG4_rep2

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

description: 93T449 cell line was established from a well-differentiated liposarcoma from the retroperitoneum of a 68 year old female.

library_source: genomic

data_processing:
reads were mapped to the human genome (hg38) using bowtie (Langmead et al., 2009).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl

molecule: genomic DNA

growth_protocol:
93T449 cells were seeded in T75 flasks in the presence of RPMI 1640 Medium supplemented with 10 % FBS and grown to 80 % confluence.
93T449 cells were routinely subcultured with a 1:2 to 1:4 ratio using Trypsin-EDTA solution and typically kept into a T75 flask of uncoated plastic in RPMI 1640 medium (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% heat inactivated FBS.

extract_protocol:
2 million cells were fixed in RPMI containing 1 % (v/v) formaldehyde (Thermo Scientific™ Pierce™  #28906) and 10 % (v/v) FBS for 10 min at RT. After 5 min quenching with 125 mM glycine, cells were pelleted and washed twice with PBS containing 10 % FBS. The flash frozen pellets were lysed for 5 min on ice in 100 μl of 50 mM tris-HCl pH 8.0, 10 mM EDTA, 0.5 % SDS and protease inhibitor cocktail. Samples were sonicated using the Covaris E220 to shear chromatin to an average size of 100-500 bp (2 % duty cycle, 105 W peak incident power, 200 cycles per burst, 25 min). Sheared chromatin was diluted 1:5 in IP-buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1 % SDS, 0.1 % Na-deoxycholate and 140 mM NaCl) supplemented with protease inhibitor cocktail. After centrifuging 10 min at 13,000g at 4 °C, the supernatant containing soluble chromatin fraction was recovered and incubated with 0.7 mg/ml RNase A (Thermo Scientific™ #EN0531) for 30 min at 37 °C. For chromatin immunoprecipitation 10 μl protein-G magnetic beads (Thermo Scientific™  Pierce™  #88848) were washed in IP-buffer and incubated with 1 μg Anti-FLAG Ab (Sigma-Aldrich #F3165) for 1 h at 4 °C on a rotating wheel. 50 μl of RNA digested chromatin were incubated with 250 ng BG4 Ab (or without for the mock negative control) for 1h at 16 °C. The anti-FLAG coated beads were washed with IP-buffer and incubated with chromatin-BG4 complex for 3 h at 4 °C on a rotating wheel. Beads were washed 4 times with IP-buffer and once in wash buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA). Elution of immonoprecipitates and chromatin crosslink reversal were performed incubating beads with 70 μl elution buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl and 0.5 % SDS) containing 0.3 mg/ml RNase A (Thermo Scientific™ Pierce™ #EN0531) for 30 min at 37 °C followed by the addition of 0.5 mg/ml proteinase K for 1h at 55 °C and 8 h at 65 °C shaking. Supernatant was then recovered and incubated for 1 additional h at 55 °C in the presence of 0.25 mg/ml proteinase K (Thermo Scientific™ #EO0491). The eluate was finally purified with SPRI AMPure XP beads (Beckman Coulter #A63881).
NEBNext Ultra II DNA library Prep Kit for Illumina, NEB

tag: genotype

tag: antibody


title: PAG122_NonInf Malaria Before Infection mRNA Year2 Sample


title: Amplicon_Plate_2_Donor_3_nextseq

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

institute: Gladstone-UCSF Institute of Genomic Immunology

data_processing:
Library strategy: Amplicon sequencing
Adapter sequences were trimmed from fastq files using cutadapt version 2.8 using default settings keeping a minimum read length of 50 bp. Insertions and deletions at each CRISPR target site were then calculated using Crispresso2 version 2.0.42 (Clement et al. 2019) with the following options "--quantification_window_size 3" and "--ignore_substitutions".
Genome_build: hg38
Supplementary_files_format_and_content: Modified amplicons

source_name: CD4+CD25- T cells

growth_protocol: Cells were grown in RPMI (Sigma, Cat # R0883) with 10% FCS (Sigma, Cat # F0926), with 100U/mL Pen-Strep (Gibco, Cat # 15140-122), 2mM L-Glutamine (Sigma, Cat # G7513), 10mM HEPES (Sigma, Cat # H0887), 1X MEM Non-essential Amino Acids (Gibco, Cat # 11140-050), 1mM Sodium Pyruvate (Gibco, Cat # 11360-070), and 50 U/mL IL-2 (Amerisource Bergen, Cat #10101641) at a concentration of 1E6 cells/mL.

extract_protocol:
On day 5 (sgRNA #1 Donor 1-3) or day 7 (sgRNA #2 Donor 1, 3) post-electroporation, genomic DNA was isolated from each sample using DNA QuickExtract (Lucigen, Cat #QE09050) according to the manufacturer’s protocol.
Primers were designed to flank each sgRNA genomic target site. Amplicons containing CRISPR edit sites were generated by adding 1.25 µL each of forward and reverse primer at 10nM to 5 µL of sample in QuickExtract, 12.5 µL of NEBNext Ultra II Q5 master mix (NEB, Cat #M0544L), and H2O to a total 25 µL reaction volume. The following PCR cycling conditions were used: 98°C for 3 minutes, 15 cycles of 94°C for 20 seconds followed by 65°C-57.5°C for 20 seconds (0.5°C incremental decreases per cycle), and 72°C for 1 minute, and a subsequent 20 cycles at 94°C for 20 seconds, 58°C for 20 seconds and 72°C for 1 minute, and a final 10 minute extension at 72°C. Samples were then diluted 1:200 and subsequently Illumina sequencing adapters and indices were added in a second PCR reaction. Indexing reactions included 1 µL of the diluted PCR1 sample, 2.5 µL of each the forward and reverse indexing primers at 10 µM each, 12.5 µL of NEB Q5 master mix, and H2O to a total 25 µL reaction volume. The following PCR cycling conditions were used: 98°C for 30 seconds, followed by 98°C for 10 seconds, 60°C for 30 seconds, and 72°C for 30 seconds for 12 cycles, and a final extension period at 72°C for 2 minutes. Samples were quantified in a 96-well plate reader using the Quant-IT DNA high sensitivity assay kit (Invitrogen, Cat #Q33232) according to the manufacturer’s protocol and pooled into 1 tube. Post pooling, samples were then SPRI purified, and quantified using an Agilent 4200 TapeStation. Samples were then sequenced on an Illumina MiniSeq or NextSeq with PE 300 reads.

treatment_protocol: GuideRNA/Cas9 ribonucleoprotein complexes were electroporated into CD4+CD25- T cells.

value: CD4+CD25- T cells


title: PAG100_Inf Malaria Symptomatic stage mRNA Year2 Sample

value: Malaria Symptomatic stage


title: IP-93T449-BG4_rep2

value: BG4 (in house purified from BG4 encoding plasmid pSANG10-3F-BG4 transformed into BL21(DE3)).


title: PAG118_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: PAG100_NonInf Malaria Before Infection mRNA Year2 Sample


title: NC

source_name: negative control of KSHV infection

value: KSHV noninfected SH-SY5Y


title: INPUT-93T449-BG4_rep1


title: Thymus - rep 2

city: Seattle

first: David

last: Hawkins

state: WA

address: 1959 NE Pacific St, HSB K226

department: Division of Medical Genetics, Department of Genome Sciences

institute: University of Washington

description: thymus.bw

data_processing:
TrimGalore (v0.4.1) was used to remove adapters
STAR (v2.6.1c) was used for alignment
deepTools bamCoverage (v3.5.0) was used to generate bigWig files
Genome_build: GRCg6a (genome-build-accession NCBI:GCA_000002315.5)
Supplementary_files_format_and_content: UCSC track format (bigWig)

organism: Gallus gallus

source_name: Thymus

extract_protocol:
Total RNA from tissues and immune cells was collected using Trizol/Chloroform. The total RNA from immune cells was DNase treated after extraction
ERCC RNA Spike-In Controls included. Libraries were pooled and sequenced on HiseqX-PE150 by Novogene Bioinformatics Technology Co
Extra Extraction Step: The total RNA from tissues was purified, and DNase treated using the Direct-zol RNA Miniprep Plus

tag: strain

value: F1 crosses of Line 6 and Line 7 from the Avian Disease and Oncology Laboratory (ADOL)

value: Thymus


title: PAG076_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: T Cell (spleen) - rep 1

source_name: T Cell (spleen)

extract_protocol:
Total RNA from tissues and immune cells was collected using Trizol/Chloroform. The total RNA from immune cells was DNase treated after extraction
ERCC RNA Spike-In Controls included. Libraries were pooled and sequenced on HiseqX-PE150 by Novogene Bioinformatics Technology Co

value: T Cell (spleen)


title: Amplicon_Plate_2_Donor_3_miniseq


title: T Cell (spleen) - rep 2


title: Amplicon_Plate_2_Donor_1_nextseq


title: Proximal Cecum - rep 2

source_name: Proximal Cecum

value: Proximal Cecum


title: OmniATAC_93T449_NT_m1

data_processing:
reads were mapped to the human genome (hg38) using bowtie (Langmead et al., 2009)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl

extract_protocol:
ATAC-seq of 93T449 cells was performed according to the Omni-ATAC protocol developed by Corces et al. 2017. Briefly, 50000 viable cells were pelleted and lysed in Resuspension buffer (Tris-HCl pH 7.4 10 mM, NaCl 10 mM, MgCl2 3 mM, NP40 0.1%, Tween-20 0.1%, digitonin 0.01% - Promega #G9441) for 3 min on ice. Next nuclei were pelleted and the transposition reaction was performed incubating the lysate for 30 min at 37 °C under agitation in the presence of Transposition mixture (Tris-HCl pH 7.6 10 mM, MgCl2 5 mM, dimethyl formamide 10%, Tn5 enzyme 100 nM – Illumina #20018704, digitonin 0.01% - Promega #G9441, Tween-20 0.1%, PBS 33%). The transposition reaction was purified (Qiagen MinElute PCR Purification kit, Qiagen #28004)
The transposed DNA was subsequently amplified in 50µl reactions with custom primers as described (Buenrostro et al., 2013). After 4 cycles libraries were then monitored with qPCR: 5 µl PCR sample in a 15 µl reaction with the same primers. qPCR output was monitored for the ΔRN; 0.25 ΔRN cycle number was used to estimate the number of additional cycles of the PCR reaction needed for the remaining PCR samples. Amplified libraries were purified with the Qiagen PCR clean-up MinElute kit (Qiagen) and size selected for fragments less than 600 bp using the Agencourt AMPure XP beads (Beckman Coulter). Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis.


title: PAG076_NonInf Malaria Before Infection mRNA Year2 Sample


title: Amplicon_Plate_2_Donor_1_miniseq


title: Amplicon_Plate_1_Donor_3_nextseq


title: Ovary - rep 2

description: ovary.bw

source_name: Ovary

value: Ovary


title: Proximal Cecum - rep 1


title: PAG074_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: Xins_30dS_rep4

city: Jena

first: Oscar

middle: Gutierrez

last: Gutierrez

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

description: Xins_30dS7dS1dS_tpms_normalized_nonfiltered.xlsx

data_processing:
Kallisto (version 0.43.0) (Bray et al., 2016) was used to perform read pseudo-alignment and quantification with the parameters –l 200 –s 20 –b 100.
TPMs (Transcripts per million) were normalized by Kallisto
Genome_build: Dresden Schmidtea mediterranea transcriptome (version 4) was used as reference (PlanMine) (Rozanski et al., 2019)
In this link you can find information about the nomenclature : http://planmine.mpi-cbg.de/planmine/user_guide.html#Naming-scheme
Supplementary_files_format_and_content: Excel file include TPMs values (Transcripts per million) for each transcript in all the samples

organism: Schmidtea mediterranea

source_name: FACS sorted cells

extract_protocol:
RNA was harvested from FACS sorted cells using Trizol LS reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: reproduction

value: Asexual

tag: days of starvation


title: Xins_30dS_rep3


title: NAM-rep3-technical2-scATAC

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description:
scATAC
Raw multiplexed NAM genotypes

data_processing:
Raw data processing with Cellranger
Cell genotyping with demuxlet
Peak calling with MACS2
Peaks filtered by empirical 0.001 FDR (using permuted background regions)
Genome_build: Zm-REFERENCE-NAM
Supplementary_files_format_and_content: NAM_lines_concatenated.ATAC.narrowpeak (column 1 = chromosome), (column 2 = start), (column 3 = end), (column 4 = peakID), (column 5 = -10*log10pvalue), (column 6 = NA), (column 7 = fold-change at peak summit), (column 8 = -log10pvalue at peak summit), (column 9 = -log10qvalue at peak summit), (column 10 = genotype), (column 11 = reference assembly)

organism: Zea mays

source_name: seedling

extract_protocol:
16,000 input nuclei per library (4 total libraries)
10X Genomics scATAC-seq v1.1

value: seedling

tag: treament

value: Frozen


title: PAG074_NonInf Malaria Before Infection mRNA Year2 Sample


title: Xins_30dS_rep2


title: Thymus - rep 1

description: thymus.bw


title: NAM-rep3-technical1-scATAC

description:
scATAC
Raw multiplexed NAM genotypes


title: PAG071_NonInf Malaria Before Infection mRNA Year2 Sample


title: Ovary - rep 1

description: ovary.bw


title: PAG071_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: NAM-rep2-scATAC

description:
scATAC
Raw multiplexed NAM genotypes

value: Fresh


title: Monocyte (blood) - rep 2

source_name: Monocyte (blood)

value: Monocyte (blood)


title: PAG060_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: Xins_7dS_rep4


title: NAM-rep1-scATAC

description:
scATAC
Raw multiplexed NAM genotypes


title: Monocyte (blood) - rep 1


title: PAG060_NonInf Malaria Before Infection mRNA Year2 Sample


title: Xins_7dS_rep3


title: Tzi8.rep4

description:
ATAC
Genotype aggregated nuclei


title: Macrophage (lung) - rep 1

source_name: Macrophage (lung)

value: Macrophage (lung)


title: PAG058_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: Tzi8.rep3

description:
ATAC
Genotype aggregated nuclei


title: Jejunum - rep 2

description: jejunum.bw

source_name: Jejunum

value: Jejunum


title: PAG058_NonInf Malaria Before Infection mRNA Year2 Sample

value: Malaria Before Infection


title: Tzi8.rep2

description:
ATAC
Genotype aggregated nuclei


title: Jejunum - rep 1

description: jejunum.bw


title: Xins_1dS_rep4


title: Xins_7dS_rep1


title: Tzi8.rep1

description:
ATAC
Genotype aggregated nuclei


title: PAG049_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: Xins_30dS_rep1


title: Xins_7dS_rep2


title: PAG049_NonInf Malaria Before Infection mRNA Year2 Sample


title: Xins_1dS_rep3


title: Tx303.rep4

description:
ATAC
Genotype aggregated nuclei


title: Macrophage (lung) - rep 2


title: PAG036_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: Xins_1dS_rep2


title: Bursa - rep 2

description: bursa.bw

source_name: Bursa

value: Bursa


title: Tx303.rep3

description:
ATAC
Genotype aggregated nuclei


title: Xins_1dS_rep1


title: Tx303.rep2

description:
ATAC
Genotype aggregated nuclei


title: PAG036_NonInf Malaria Before Infection mRNA Year2 Sample


title: PAG035_Inf Malaria Symptomatic stage mRNA Year2 Sample

value: Malaria Symptomatic stage


title: Bursa - rep 1

description: bursa.bw


title: PAG035_NonInf Malaria Before Infection mRNA Year2 Sample


title: X2_30dS_rep4

description: X2_30dS7dS1dS_tpms_normalized_nonfiltered.xlsx


title: P39.rep4

description:
ATAC
Genotype aggregated nuclei


title: X2_30dS_rep3


title: Ileum - rep 2

description: ileum.bw

source_name: Ileum

value: Ileum


title: B Cell - rep 1

description: bcell.bw

source_name: B Cell

value: B Cell


title: PAG034_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: X2_30dS_rep2


title: Soybean_10days_tis_leaf_H3K4me3

description: Chip sample

data_processing:
Reads were trimmed using trimmomatic, and aligned to the genome using bowtie2, `--very-sensitive`. Only uniquely mapping reads were used for downstream analysism, with duplicates being removed using the picard MarkDuplicates command.
 Peak calling was done for histone modifications known to have broad peaks (H3K36me3, and H3K4me1) using the software epic2 with the parameters “--false-discovery-rate-cutoff .1 --keep-duplicates”, as well as MACS2 to identify smaller regions of enrichment using the parameters `callpeak --keep-dup all -g 1.6e9 -q .1`. Narrow peaks (H3K56ac and H3K4me3) were called using MACS2 with the parameters “ --keep-dup all --extsize 147 -g 1.6e9 -p .05’ (Stovner and Sætrom, 2019, p. 2; Zhang et al., 2008). Peaks which were within 480 bps, or roughly two nucleosomes of each other were merged. Intersection between replicates of the same histone modification were taken, and the total length of the two overlapping segments were taken.
Genome_build: Z. mays genome and gene annotation AGPv4
Supplementary_files_format_and_content: bed files. Column1: Chromosome; Column2: Start of Peak; Column3: End of peak

organism: Glycine max

source_name: leaf

growth_protocol: Glycine max (accession William82) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). The 2nd and 3rd leaves were collected for the experiments. For Zea mays Ear primordia protocol: Plants were grown in greenhouse or field conditions. Plants were harvested approximately one month after sowing and ear primordia were dissected from shoots. Ear primordia were harvested from any node of the shoot if they were within the desired size range: between 3 to 8 millimeters from the base to the apical tip of the ear.

extract_protocol:
ChiP-seq was performed following the methods of (Zang et al. 2007). Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation
Antibidies Used: Anti-trimethyl-Histone H3 (Lys4) [EMD Millipore, Cat#:07-473],   Anti-Histone H3 (tri methyl K36) [Abcam, Cat#:ab9050], Anti-acetyl-Histone H3 (Lys56) [EMD Millipore, Cat#:07-677-I]

treatment_protocol: No Treatmant

value: leaf

tag: chip antibody


title: X2_30dS_rep1


title: P39.rep2

description:
ATAC
Genotype aggregated nuclei


title: PAG034_NonInf Malaria Before Infection mRNA Year2 Sample


title: P39.rep3

description:
ATAC
Genotype aggregated nuclei


title: Ileum - rep 1

description: ileum.bw

value: F1 crosses of Line 6 and Line 7 from the Avian Disease and Oncology Laboratory (ADOL)


title: X2_7dS_rep4


title: P39.rep1

description:
ATAC
Genotype aggregated nuclei


title: X2_7dS_rep3


title: OH7B.rep4

description:
ATAC
Genotype aggregated nuclei


title: PAG031_NonInf Malaria Before Infection mRNA Year2 Sample


title: PAG031_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: Tx303.rep1

description:
ATAC
Genotype aggregated nuclei


title: Leaf177_vitro_3 TN_B_040

city: Cologne

first: Tatsuya

last: Nobori

address: Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research

description:
Leaf177_vitro_3
Proteobacteria
L177_combined.txt

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the  genome of corresponding commensal strain using Bowtie2 (version 2.2.8) with the parameters -p 20 -q --phred33 and transformed into a count per gene per library by using HTSeq (version 0.6.0).
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Burkholderia sp. Leaf177

source_name: Bacteria isolated from Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.

extract_protocol:
RNA was isolated from bacterial cells using FastRNA PRO™ BLUE KIT (MP Biomedicals). For plant RNA-seq, RNA was extracted with FastRNA PRO™ KIT with Lysing Matrix E (MP Biomedicals) and DNA was digested with TURBO DNase (Ambion). RNA quality was determined using a 2100 Bioanalyzer (Agilent Technologies, USA). 500 ng total RNA has initially been used for polyA enrichment with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
For bacterial RNA-seq, cDNA libraries were generated with Ovation Complete Prokaryotic RNA-Seq kit 1-8 (NuGEN). For plant RNA-seq, cDNA libraries were generated from polyA enriched RNA using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Commensal strains were grown in the liquid 50% TSB medium. For each strain, multiple cultures were prepared with different bacterial density to ensure that unsaturated cultures are used for experiments. Bacterial cells were harvested by centrifugation, washed twice with sterile water, and resuspended in sterile water to OD600 of 0.5 (∼2.5 × 108 cfu/mL). For bacterial RNA-seq, 80–100 A. thaliana leaves (four fully expanded leaves per plant) were syringe-inoculated with bacterial suspensions using a needleless syringe. For plant RNA-seq, approximately six leaves (two fully expanded leaves per plant) were treated. Mock control (water infiltration) was included in every experiment. Leaves were harvested at 6 hours after inoculation. Sampling was conducted for each plant genotype at a time, and it took approximately 5 min per genotype. Leaves were immediately frozen in liquid nitrogen, and stored at -80°C.

tag: host genotype

tag: replicate


title: X2_7dS_rep2


title: OH7B.rep3

description:
ATAC
Genotype aggregated nuclei


title: B Cell - rep 2

description: bcell.bw


title: Leaf177_col_2 TN_B_031

institute: Max-Planck Institute for Plant Breeding Research

description:
Leaf177_col_2
Proteobacteria
L177_combined.txt


title: Leaf177_col_1 TN_B_030

description:
Leaf177_col_1
Proteobacteria
L177_combined.txt


title: PAG030_NonInf Malaria Before Infection mRNA Year2 Sample

source_name: Blood


title: X2_7dS_rep1


title: OH7B.rep2

description:
ATAC
Genotype aggregated nuclei


title: PAG029_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: Leaf177_vitro_2 TN_B_019

description:
Leaf177_vitro_2
Proteobacteria
L177_combined.txt


title: OH7B.rep1

description:
ATAC
Genotype aggregated nuclei


title: Leaf177_col_3 TN_B_051

description:
Leaf177_col_3
Proteobacteria
L177_combined.txt


title: X2_1dS_rep4


title: Leaf177_vitro_1 TN_B_018

description:
Leaf177_vitro_1
Proteobacteria
L177_combined.txt


title: X2_1dS_rep3


title: Oh43.rep1

description:
ATAC
Genotype aggregated nuclei


title: Oh43.rep2

description:
ATAC
Genotype aggregated nuclei


title: X2_1dS_rep2


title: PAG029_NonInf Malaria Before Infection mRNA Year2 Sample


title: Leaf130_vitro_3 TN_B_037

description:
Leaf130_vitro_3
Proteobacteria
L130_combined.txt

organism: Acinetobacter sp. Leaf130


title: Leaf130_col_3 TN_B_052

description:
Leaf130_col_3
Proteobacteria
L130_combined.txt


title: PAG030_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: X2_1dS_rep1


title: PAG016_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: NC358.rep4

description:
ATAC
Genotype aggregated nuclei


title: NC358.rep3

description:
ATAC
Genotype aggregated nuclei


title: Leaf130_col_2 TN_B_029

description:
Leaf130_col_2
Proteobacteria
L130_combined.txt


title: X1_30dS_rep4

description: X1_30dS7dS1dS_tpms_normalized_nonfiltered.xlsx


title: X1_30dS_rep3


title: Leaf130_col_1 TN_B_028

description:
Leaf130_col_1
Proteobacteria
L130_combined.txt


title: PAG021_NonInf  Malaria Before Infection mRNA Year2 Sample


title: Leaf130_vitro_2 TN_B_013

description:
Leaf130_vitro_2
Proteobacteria
L130_combined.txt


title: NC358.rep2

description:
ATAC
Genotype aggregated nuclei


title: X1_30dS_rep2


title: NC358.rep1

description:
ATAC
Genotype aggregated nuclei


title: Leaf130_vitro_1 TN_B_012

description:
Leaf130_vitro_1
Proteobacteria
L130_combined.txt


title: X1_30dS_rep1


title: PAG021_Inf  Malaria Symptomatic stage mRNA Year2 Sample


title: PAG007_NonInf  Malaria Before Infection mRNA Year2 Sample


title: NC350.rep4

description:
ATAC
Genotype aggregated nuclei


title: Leaf187_col_3 TN_B_049

description:
Leaf187_col_3
Firmicutes
L187_combined.txt

organism: Exiguobacterium sp. Leaf187


title: Pt92_BRD4_1UM

city: Tampa

first: Jianguo

last: Tao

state: Florida

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

data_processing:
RNA sequencing was performed on HiSeq 2500v4 high output (50-bp, single-end reads)
Tophat2 was used to align the Fasq files.
TPM values were calculated and normalized using Cuffnorm
Genes that had a p < 0.05 and at least a two-fold change were considered to be significantly altered between treatments.
Cutoff value for expressed genes was TPM value equal to or higher than 1.
Genome_build: hg38
Supplementary_files_format_and_content: excel

source_name: Mantle cell lympohoma_NVP-2

growth_protocol: Primary patient tumor cells was collected and frozen after treatment.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini (Qiagen Cat# 74134)
Library prep was conducted using TruSeq Stranded mRNA Library Prep Kit (Illumina Cat #RS-122-2101/2) according to the manufacturer’s instructions

treatment_protocol: NVP-2 or INCB054329 at indicated concentration was added to cell suspesion and treated overnight

tag: sample id

value: primary patient mantle cell lympohoma cells


title: Leaf187_vitro_3 TN_B_041

description:
Leaf187_vitro_3
Firmicutes
L187_combined.txt


title: X1_7dS_rep4


title: X1_7dS_rep3


title: NC350.rep3

description:
ATAC
Genotype aggregated nuclei


title: Pt92_DMSO


title: Pt92_BRD4_200


title: X1_7dS_rep2


title: Leaf187_vitro_2 TN_B_021

description:
Leaf187_vitro_2
Firmicutes
L187_combined.txt


title: X1_7dS_rep1


title: NC350.rep2

description:
ATAC
Genotype aggregated nuclei


title: PAG016_NonInf  Malaria Before Infection mRNA Year2 Sample


title: Leaf187_vitro_1 TN_B_020

description:
Leaf187_vitro_1
Firmicutes
L187_combined.txt


title: Pt92_NVP2_50


title: NC350.rep1

description:
ATAC
Genotype aggregated nuclei


title: PAG007_Inf Malaria Symptomatic stage mRNA Year2 Sample


title: Ms71.rep3

description:
ATAC
Genotype aggregated nuclei


title: Ms71.rep4

description:
ATAC
Genotype aggregated nuclei


title: Pt92_NVP2_250


title: X1_1dS_rep4


title: Leaf187_col_2 TN_B_008

description:
Leaf187_col_2
Firmicutes
L187_combined.txt


title: X1_1dS_rep3


title: X1_1dS_rep2


title: Pt91_NVP2_250


title: Ms71.rep1

description:
ATAC
Genotype aggregated nuclei


title: Leaf404_col_3 TN_B_050

description:
Leaf404_col_3
Bacteroidetes
L404_combined.txt

organism: Chryseobacterium sp. Leaf404


title: Leaf187_col_1 TN_B_007

description:
Leaf187_col_1
Firmicutes
L187_combined.txt


title: Ms71.rep2

description:
ATAC
Genotype aggregated nuclei


title: Leaf404_vitro_3 TN_B_042

description:
Leaf404_vitro_3
Bacteroidetes
L404_combined.txt


title: X1_1dS_rep1


title: Mo18W.rep2

description:
ATAC
Genotype aggregated nuclei


title: Pt91_DMSO

source_name: Mantle cell lympohoma_DMSO

value: DMSO


title: Pt91_BRD4_200

source_name: Mantle cell lympohoma_INCB0543296


title: Leaf404_vitro_2 TN_B_023

description:
Leaf404_vitro_2
Bacteroidetes
L404_combined.txt


title: Leaf404_vitro_1 TN_B_022

description:
Leaf404_vitro_1
Bacteroidetes
L404_combined.txt


title: Pt91_BRD4_1UM

source_name: Mantle cell lympohoma_INCB054329


title: Mo18W.rep1

description:
ATAC
Genotype aggregated nuclei


title: M37W.rep4

description:
ATAC
Genotype aggregated nuclei


title: cct3_RNAi_72hR_rep3

data_processing:
Kallisto (version 0.43.0) (Bray et al., 2016) was used to perform read pseudo-alignment and quantification with the parameters –l 200 –s 20 –b 100.
TPMs (Transcripts per million) were normalized by Kallisto
Genome_build: Dresden Schmidtea mediterranea transcriptome (version 4) was used as reference (PlanMine) (Rozanski et al., 2019)
In this link you can find information about the nomenclature : http://planmine.mpi-cbg.de/planmine/user_guide.html#Naming-scheme

IDs numbers from Dresden transcriptome of version 4 are equivalent to version 6 (Planmine). For example, dresden_comp15_c0_seq1 is equivalent to dd_Smed_v6_15_0_1.
Supplementary_files_format_and_content: Excel file include TPMs values (Transcripts per million) for each transcript in all the samples

source_name: whole planarian

extract_protocol:
RNA was harvested from 5 regenerating trunks/sample using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: cct3_RNAi_72hR_rep2


title: Leaf404_col_2 TN_B_009

description:
Leaf404_col_2
Bacteroidetes
L404_combined.txt


title: Leaf404_col_1 TN_B_005

description:
Leaf404_col_1
Bacteroidetes
L404_combined.txt


title: PT90_NVP2_250


title: gfp_RNAi_72hR_rep3

value: gfp(RNAi)


title: Pt91_NVP2_50


title: Pt90_DMSO


title: cct3_RNAi_72hR_rep1

value: Asexual


title: parental wild type strain sensitive to Congo Red Rep3 [ku80-CT4]

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs).  Only sequences at least 25 nt in length were considered for further analysis.
Tophat version 1.4.1.1, with default parameters, was used for alignment on the reference genome
Genes were counted using HTSeq-count version 0.6.1  (parameters: -t exon -i gene_id  ).
The change of gene expression level was calculated as the logarithm to base 2 of the fold change of the gene reads in the medium with CR vs the medium without CR. In addition, the gene expression of single strains was compared at high and low CR concentration. Count data were analyzed separately for "Low", "High" and parental and mutant samples using the Bioconductor package DESeq2 version 1.8.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the different biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed
Genome_build: Aspergillus fumigatus A1163
Supplementary_files_format_and_content: Matrix from DESeq2
Supplementary_files_format_and_content: ku80_vs_1D4_vs_2C7.complete.txt

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: growth of the fungus in liquid MM medium in shaken flasks at 150 rpm

extract_protocol:
Mycelium was flash frozen in liquid nitrogen. RNA extraction was carried out using a  phenol-chloroform based method and quality of the total RNA from three independent replicates was checked on the Bioanalyzer system (Agilent)
Poly-adenylated RNA purification and indexed libraries were performed using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina).

treatment_protocol: growth in presence or absence of Congo Red (300 microg per ml) for 4 days

value: parental wild type

tag: phenotype

value: sensitive to Congo Red

tag: agent

value: Congo Red 0µgCR/ml

tag: growth protocol

value: Growth for 4 days in absence of CR


title: gfp_RNAi_72hR_rep2


title: M37W.rep1

description:
ATAC
Genotype aggregated nuclei

tag: tissue

value: seedling

value: Fresh


title: PT90_BRD4_200

tag: cell type

tag: treatment


title: parental wild type strain sensitive to Congo Red Rep2 [ku80-CT3]

tag: genotype


title: M162W.rep4

description:
ATAC
Genotype aggregated nuclei

value: Frozen


title: Het2 Cerebellum

city: Seoul

first: Joon Yong

last: An

address: 145 Anam-ro, Anam-dong, Seongbuk-gu

country: South Korea

institute: Korea University

description: *** Submitter declaration: "We lost our fastq files for the analysis so we are able to submit only processed data files for submission." ***

data_processing: After trimming low-quality bases, the sequence reads were aligned using the STAR algorithm. Then, we quantified gene expression using the StringTie, resulting 16,447 genes expressed in cerebellum tissues.

organism: Mus musculus

extract_protocol: We obtained two WT and two Kdm3b+/- mice samples for RNA-sequencing analysis.

value: cerebellum

value: heterozygous Kdm3b


title: Pt90_BRD4_1uM


title: gfp_RNAi_72hR_rep1


title: M162W.rep3

description:
ATAC
Genotype aggregated nuclei


title: Pt88_NVP2_50


title: parental wild type strain sensitive to Congo Red Rep3 [ku80-CR3]

value: Congo Red 300 µgCR/ml

value: Growth for 4 days in presence of CR


title: parental wild type strain sensitive to Congo Red Rep2 [ku80-CR2]


title: PT90_NVP2_50


title: parental wild type strain sensitive to Congo Red Rep1 [ku80-CT2]


title: M37W.rep3

description:
ATAC
Genotype aggregated nuclei


title: M162W.rep1

description:
ATAC
Genotype aggregated nuclei


title: Het1 Cerebellum


title: Pt88_NVP2_250


title: M37W.rep2

description:
ATAC
Genotype aggregated nuclei


title: parental wild type strain sensitive to Congo Red Rep1 [ku80-CR1]


title: WT2 Cerebellum

value: Wild Type


title: WT1 Cerebellum


title: Ky21.rep4

description:
ATAC
Genotype aggregated nuclei


title: Pt88_DMSO


title: Pt88_BRD4_200

source_name: Mantle cell lympohoma_INCB0543329


title: Ky21.rep3

description:
ATAC
Genotype aggregated nuclei

source_name: seedling


title: Mutant resistant to Congo Red Rep2 [2C7-CT2]

description: Growth for 4 days in absence of CR

tag: bacterial strain

value: Congo Red 0microgCR/ml


title: Mutant resistant to Congo Red Rep3 [2C7-CT3]

description: Growth for 4 days in absence of CR


title: Ky21.rep2

description:
ATAC
Genotype aggregated nuclei


title: Mutant resistant to Congo Red Rep1 [2C7-CT1]

description: Growth for 4 days in absence of CR


title: Donor_4_ZNF217_F10_ATAC

data_processing:
Adapters were trimmed from fastq files using cutadapt version 2.10 with default settings keeping a minimum read length of 20 bp. Reads were then mapped to the human genome GRCh38 using bowtie2 version 2.4.1 with the following settings “-X 2000 --very-sensitive”. Low quality reads were filtered using samtools version 1.10 using the following command “samtools view -h -b -F 1804 -f 2 -q 30”. Reads mapping within the ENCODE blacklist region were removed using bedtools version 2.29.2 using bedtools intersect. Duplicated reads were removed using picard version 2.23.3 using the following settings “VALIDATION_STRINGENCY=LENIENT”. Reads mapping to ChrX, ChrY, and ChrM were excluded from further analysis. Reads were converted to single nucleotide ATAC insertion sites using the following command “bedtools bamtobed -i {input.bam} | awk 'BEGIN {{OFS = "\t"}} $6 == "+" {{$2 = $2 + 4; $3 = $2 + 1; print}} $6 == "-" {{$3 = $3 - 4; $2 = $3 - 1; print}}' | sort -k1,1 -k2,2n > {output.bed}”. For each sample, peaks were called using macs2 version 2.2.7.1 using the ATAC insertion site bed files as input with the following settings “--format BED --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -B --SPMR -q 0.01”.     Peaks called in individual samples were merged into a consensus peak file in the following way using single nucleotide peak summits from macs2. For each KO or control condition, peak summits that were within 75 bp of another peak summit in two out of three donors and were supported by at least 10 ATAC-Seq reads were merged into reproducible summit clusters. Across all samples, reproducible summits from each KO or controls were aggregated with other summits within 150 bp of each other. For each aggregate cluster, we calculated an average summit location based on the location of all of the summits within the cluster. Each average summit location was then extended to 350 bp peaks centered on the average summit location to generate a consensus peak list. For each sample, the number of ATAC-Seq insertion sites that overlap each consensus peak was counted using the summarizeOverlaps function in the GenomicAlignments package.
Genome_build: hg38
Supplementary_files_format_and_content: Count of ATAC insertion sites within peaks.

source_name: CD4+CD25- T cells

extract_protocol:
We harvested, counted, and treated each T cell culture with 200U/mL of DNase (Worthington Cat # LS002007) for 30 mins at 37 degrees. We then transferred 60,000 cells of each T cell culture into individual wells of a 96-well plate and washed cells once with PBS and once with RSB (10mM Tris HCl pH 7.5, 10mM NaCl, 3mM MgCl2). Cells were lysed in 50uL of cell lysis buffer (0.1% NP40, 0.1% Tween-20, 0.01% Digitonin in RSB) on ice for 3 min.
To the cell lysate, we then added 150ul of RSB with 0.1% Tween-20 to each well and pelleted nuclei at 500g for 10 min at 4 degree. Cells were resuspended in 50ul transposition mix (25ul 2X TD buffer, 16.5ul 1X PBS, 0.5ul 10% Tween, 0.5ul 1% Digitonin, 2.5ul Tn5 transposase, and 5ul H2O) and transposition was performed at 37 degrees for 30 min with 300rpm shaking. Transposed fragments were purified using ZR-96 DNA Clean & Concentrator-5 Kit (Zymo D4024) and libraries were generated using PCR amplification with Nextera adapters and purified using Ampure beads. ATAC-Seq libraries were sequenced on a Novaseq with paired end 100 bp reads.

treatment_protocol: CD4+CD25- T cells were isolated from 3 donors using consented Luekopaks (STEMCELL). Guide RNAs against 24 targets or 8 AAVS1 controls were assembled into Cas9 ribonucleoproteins and electroporated into the cells. Five days after electroporation cells were collected.

value: CD4+CD25- T cells


title: Pt92

value: primary patient mantle cell lympohoma cells

value: DMSO


title: M162W.rep2

description:
ATAC
Genotype aggregated nuclei


title: Ky21.rep1

description:
ATAC
Genotype aggregated nuclei


title: Donor_4_TNFAIP3_G4_ATAC


title: Pt91


title: KI3.rep4

description:
ATAC
Genotype aggregated nuclei


title: Mutant resistant to Congo Red Rep3 [2C7-CR4]

description: Growth for 4 days in presence of CR

value: Congo Red 300 microgCR/ml


title: Mutant resistant to Congo Red Rep2 [2C7-CR3]

description: Growth for 4 days in presence of CR


title: Donor_4_STAT5B_G2_ATAC


title: KI3.rep3

description:
ATAC
Genotype aggregated nuclei


title: Pt90


title: Donor_4_RELA_F6_ATAC


title: Pt89


title: Mutant resistant to Congo Red Rep3 [1D4-CT3]

description: Growth for 4 days in absence of CR


title: KI3.rep1

description:
ATAC
Genotype aggregated nuclei


title: KI3.rep2

description:
ATAC
Genotype aggregated nuclei


title: Mutant resistant to Congo Red Rep1 [2C7-CR1]

description: Growth for 4 days in presence of CR


title: Mutant resistant to Congo Red Rep2 [1D4-CT2]

description: Growth for 4 days in absence of CR


title: Pt88_BRD4_1uM


title: Donor_4_STAT5A_G7_ATAC


title: Pt87


title: Pt86


title: Donor_4_PTEN_F11_ATAC


title: Donor_4_YY1_G6_ATAC


title: Pt84


title: Donor_4_MED12_H5_ATAC


title: Ki11.rep4

description:
ATAC
Genotype aggregated nuclei


title: Donor_4_MYB_G5_ATAC


title: Ki11.rep3

description:
ATAC
Genotype aggregated nuclei


title: Mutant resistant to Congo Red Rep1 [1D4-CT1]

description: Growth for 4 days in absence of CR


title: Mutant resistant to Congo Red Rep3 [1D4-CR4]

description: Growth for 4 days in presence of CR


title: Pt83


title: Ki11.rep2

description:
ATAC
Genotype aggregated nuclei


title: Mutant resistant to Congo Red Rep2 [1D4-CR3]

description: Growth for 4 days in presence of CR


title: Pt81


title: Donor_4_MBD2_H8_ATAC


title: Donor_4_KMT2A_H6_ATAC


title: Ki11.rep1

description:
ATAC
Genotype aggregated nuclei


title: Mutant resistant to Congo Red Rep1 [1D4-CR1]

description: Growth for 4 days in presence of CR


title: Donor_4_KLF2_F8_ATAC


title: Il14H.rep4

description:
ATAC
Genotype aggregated nuclei


title: Pt80


title: Pt76


title: Il14H.rep3

description:
ATAC
Genotype aggregated nuclei


title: Pt39


title: Donor_4_IRF4_H11_ATAC


title: Pt38


title: WT-l-CT3

description: Growth for 4 h in absence of CR

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs).  Only sequences at least 25 nt in length were considered for further analysis.
Tophat version 1.4.1.1, with default parameters, was used for alignment on the reference genome
Genes were counted using HTSeq-count version 0.6.1  (parameters: -t exon -i gene_id  ).
The change of gene expression level was calculated as the logarithm to base 2 of the fold change of the gene reads in the medium with CR vs the medium without CR. In addition, the gene expression of single strains was compared at high and low CR concentration. Count data were analyzed separately for "Low", "High" and parental and mutant samples using the Bioconductor package DESeq2 version 1.8.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the different biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed
Genome_build: Aspergillus fumigatus A1163
Supplementary_files_format_and_content: Matrix from DESeq2

source_name: Parental strain rep2

value: parental strain

tag: strain

tag: growth

value: 0 µg/ml CR


title: WT-l-CT1

description: Growth for 4 h in absence of CR

source_name: Parental strain rep1


title: Donor_4_IRF2_G10_ATAC


title: Il14H.rep2

description:
ATAC
Genotype aggregated nuclei


title: Il14H.rep1

description:
ATAC
Genotype aggregated nuclei


title: WT-l-CR4

description: Growth for 4 h in presence of CR

source_name: Parental strain rep3

value: 50 µg/ml CR


title: Pt72


title: Donor_4_IRF1_H4_ATAC


title: HP301.rep4

description:
ATAC
Genotype aggregated nuclei


title: WT-l-CR2

description: Growth for 4 h in presence of CR


title: Donor_4_IL2RA_H1_ATAC


title: Pt66


title: HP301.rep3

description:
ATAC
Genotype aggregated nuclei


title: WT-l-CR1

description: Growth for 4 h in presence of CR


title: Pt64


title: WT-h-CT4

description: Growth for 4 h in absence of CR


title: WT-l-CT4

description: Growth for 4 h in absence of CR


title: Pt63


title: Donor_4_JAK3_H3_ATAC


title: HP301.rep1

description:
ATAC
Genotype aggregated nuclei


title: WT-h-CT2

description: Growth for 4 h in absence of CR


title: Donor_4_GATA3_F9_ATAC


title: HP301.rep2

description:
ATAC
Genotype aggregated nuclei


title: WT-h-CT1

description: Growth for 4 h in absence of CR


title: CML69.rep4

description:
ATAC
Genotype aggregated nuclei


title: Pt61


title: Pt62


title: CML69.rep3

description:
ATAC
Genotype aggregated nuclei


title: Pt60


title: Donor_4_FOXK1_F12_ATAC


title: WT-h-CR3

description: Growth for 4 h in presence of CR

value: 300 µg/ml CR


title: CML69.rep2

description:
ATAC
Genotype aggregated nuclei

value: seedling


title: Pt59


title: WT-h-CR2

description: Growth for 4 h in presence of CR


title: WT-h-CR1

description: Growth for 4 h in presence of CR


title: CML69.rep1

description:
ATAC
Genotype aggregated nuclei

value: Fresh


title: Donor_4_HIVEP2_G9_ATAC


title: Pt58


title: Donor_4_CBFB_H12_ATAC


title: CML52.rep4

description:
ATAC
Genotype aggregated nuclei

value: Frozen


title: Donor_4_ATXN7L3_H9_ATAC


title: CML52.rep3

description:
ATAC
Genotype aggregated nuclei


title: Pt55


title: G9-l-CT3

description: Growth for 4 h in absence of CR

source_name: Mutant sensitive to Congo Red Rep2

value: sensitive to Congo Red


title: Pt5


title: Donor_4_AAVS1_7_G3_ATAC


title: G9-l-CT2

description: Growth for 4 h in absence of CR

source_name: Mutant sensitive to Congo Red Rep1


title: CML52.rep1

description:
ATAC
Genotype aggregated nuclei


title: Donor_4_FOXP1_G12_ATAC


title: Donor_4_AAVS1_6_G8_ATAC


title: Donor_4_AAVS1_5_G11_ATAC


title: Donor_4_ETS1_H10_ATAC


title: G9-l-CR3

description: Growth for 4 h in presence of CR


title: G9-l-CR4

description: Growth for 4 h in presence of CR

source_name: Mutant sensitive to Congo Red Rep3


title: Pt45


title: Donor_4_AAVS1_4_F5_ATAC


title: Pt42


title: G9-l-CT4

description: Growth for 4 h in absence of CR


title: G9-l-CR2

description: Growth for 4 h in presence of CR


title: CML333.rep3

description:
ATAC
Genotype aggregated nuclei


title: Pt7


title: Pt35


title: CML333.rep4

description:
ATAC
Genotype aggregated nuclei


title: Donor_4_AAVS1_2_F7_ATAC


title: CML333.rep1

description:
ATAC
Genotype aggregated nuclei


title: CML333.rep2

description:
ATAC
Genotype aggregated nuclei


title: CML52.rep2

description:
ATAC
Genotype aggregated nuclei


title: Donor_4_AAVS1_3_H2_ATAC


title: Donor_4_AAVS1_8_G1_ATAC


title: Pt25


title: Donor_4_AAVS1_1_H7_ATAC


title: F4-l-CT2

description: Growth for 4 h in absence of CR


title: Donor_3_ZNF217_D2_ATAC


title: F4-l-CT3

description: Growth for 4 h in absence of CR


title: Pt21_BRD4i_500nM


title: CML322.rep4

description:
ATAC
Genotype aggregated nuclei


title: CML322.rep3

description:
ATAC
Genotype aggregated nuclei


title: Pt21


title: CML322.rep2

description:
ATAC
Genotype aggregated nuclei


title: F4-l-CR4

description: Growth for 4 h in presence of CR


title: F4-l-CR3-I5

description: Growth for 4 h in presence of CR


title: Pt13


title: F4-l-CT4

description: Growth for 4 h in absence of CR


title: Donor_3_TNFAIP3_D8_ATAC


title: Donor_3_YY1_D10_ATAC


title: F4-l-CR1

description: Growth for 4 h in presence of CR


title: Pt31


title: Pt10


title: Pt24_BRD4_500


title: CML277.rep4

description:
ATAC
Genotype aggregated nuclei


title: Donor_3_STAT5A_D11_ATAC


title: D4-h-CT4

description: Growth for 4 h in absence of CR

source_name: Mutant resistant to Congo Red Rep3

value: resistant to Congo Red


title: Donor_3_RELA_C10_ATAC


title: CML277.rep3

description:
ATAC
Genotype aggregated nuclei


title: D4-h-CT3

description: Growth for 4 h in absence of CR

source_name: Mutant resistant to Congo Red Rep2


title: CML277.rep2

description:
ATAC
Genotype aggregated nuclei


title: Donor_3_PTEN_D3_ATAC


title: D4-h-CT2

description: Growth for 4 h in absence of CR

source_name: Mutant resistant to Congo Red Rep1


title: Donor_3_MYB_D9_ATAC


title: CML277.rep1

description:
ATAC
Genotype aggregated nuclei


title: Pt24

source_name: Mantle cell lympohoma_DMSO


title: Pt22_BRD4_500nM


title: CML247.rep4

description:
ATAC
Genotype aggregated nuclei


title: D4-h-CR4

description: Growth for 4 h in presence of CR


title: Donor_3_MED12_E9_ATAC


title: D4-h-CR3

description: Growth for 4 h in presence of CR


title: Pt22


title: Donor_3_MBD2_E12_ATAC


title: CML247.rep3

description:
ATAC
Genotype aggregated nuclei


title: CML322.rep1

description:
ATAC
Genotype aggregated nuclei


title: Pt17


title: D4-h-CR2

description: Growth for 4 h in presence of CR


title: CML247.rep2

description:
ATAC
Genotype aggregated nuclei


title: CML247.rep1

description:
ATAC
Genotype aggregated nuclei


title: C7-h-CT2

description: Growth for 4 h in absence of CR


title: C7-h-CT3

description: Growth for 4 h in absence of CR


title: Donor_3_KLF2_C12_ATAC


title: Donor_3_KMT2A_E10_ATAC


title: SS.NVP2.20.6.2 [RNA-seq]

data_processing:
RNA sequencing was performed on HiSeq 2500v4 high output (50-bp, single-end reads)
Tophat2 was used to align the Fasq files.
TPM values were calculated and normalized using Cuffnorm
Genes that had a p < 0.05 and at least a two-fold change were considered to be significantly altered between treatments.
Cutoff value for expressed genes was TPM value equal to or higher than 1.
Genome_build: hg38
Supplementary_files_format_and_content: TPM values higher then 1 were shown in "IR_RMAseq_TPM.csv" file

source_name: SP49-Sen_NVP-2 20nM_6hr

growth_protocol: Jeko-1 and  SP49 parental ibrutinib sensitive cells were grown in RPMI-1640 medium with 10% FBS and treated with vehicle control or escalating dose of ibrutinib for approximately 6 months.Drug-resistant variants were maintained in drug free media for 1 week before utilized in experiments. MCL cells exposed to DMSO were maintained in parallel and used for comparison with their respective drug-resistant cell lines

treatment_protocol: 1uM ibrutinib was used in Jeko-1 IR and sensitive cells and 10nM ibrutinib was used for SP49 cells. BRD4 inhibitor INCB054329 was  used at 500nM for 48hrs for both cells. NVP-2 20nM was used at 6hrs and 48hrs for all cell lines treatment. DMSO was used as vehicle control.

tag: cell line

value: Mantle cell lympohoma

tag: group

tag: ibrutnib sensitivity

value: sensitive

value: NVP-2 20nM

tag: treatment time


title: SS.NVP2.20.6.3 [RNA-seq]


title: CML228.rep4

description:
ATAC
Genotype aggregated nuclei

tag: treament


title: Donor_3_JAK3_E7_ATAC


title: Donor_3_IRF4_F3_ATAC


title: SS.NVP2.20.6.1 [RNA-seq]


title: Pt32

tag: sample id


title: C7-h-CT1

description: Growth for 4 h in absence of CR


title: SS.NVP2.20.48.3 [RNA-seq]

source_name: SP49-Sen_NVP-2 20nM_48hr


title: C7-h-CR4

description: Growth for 4 h in presence of CR


title: CML228.rep2

description:
ATAC
Genotype aggregated nuclei


title: Donor_3_IRF2_E2_ATAC


title: SS.NVP2.20.48.2 [RNA-seq]


title: Donor_3_IRF1_E8_ATAC


title: C7-h-CR1

description: Growth for 4 h in presence of CR


title: Donor_3_IL2RA_E5_ATAC


title: CML103.rep4

description:
ATAC
Genotype aggregated nuclei


title: SS.NVP2.20.48.1 [RNA-seq]


title: wat_5 (SHAM-6h)

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Kallisto
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited Raw counts for every gene and samples
Supplementary_files_format_and_content: Tab-delimited TPM counts for every gene and samples
Supplementary_files_format_and_content: Metadata Summary of each samples

source_name: wat

extract_protocol:
Samples were snap-frozen in liquid nitrogen and stored at -80°C until analysis. Total RNA was isolated from homogenized heart tissue using RNeasy Mini Kit or RNeasy Lipid Tissue Mini Kit (Qiagen).
RNA sequencing library were prepared with Illumina RNA-Seq with Poly-A selections

value: wat

tag: age

value: 10 weeks

tag: protocol

value: SHAM

tag: time point


title: Donor_3_HIVEP2_E1_ATAC

value: CD4+CD25- T cells


title: CML103.rep3

description:
ATAC
Genotype aggregated nuclei


title: wat_41 (SHAM-6h)


title: wat_44 (MI-6h)

value: Myocardial infarction


title: SS.INC.500.48.2 [RNA-seq]


title: Donor_3_GATA3_D1_ATAC


title: SS.INC.500.48.3 [RNA-seq]


title: SS.INC.500.48.1 [RNA-seq]


title: CML103.rep1

description:
ATAC
Genotype aggregated nuclei


title: Donor_3_FOXP1_E4_ATAC


title: CML228.rep3

description:
ATAC
Genotype aggregated nuclei


title: B97.rep4

description:
ATAC
Genotype aggregated nuclei


title: Donor_3_FOXK1_D4_ATAC


title: C7-h-CR3

description: Growth for 4 h in presence of CR

tag: phenotype


title: B97.rep3

description:
ATAC
Genotype aggregated nuclei

tag: tissue


title: Donor_3_ETS1_F2_ATAC

tag: cell type


title: SS.IB.INC.48.3 [RNA-seq]

tag: treatment


title: SS.IB.INC.48.1 [RNA-seq]


title: SS.IB.INC.48.2 [RNA-seq]


title: wat_35 (SHAM-6h)


title: Donor_3_CBFB_F4_ATAC


title: wat_34 (MI-24h)


title: SS.IB.1UM.48.3 [RNA-seq]

source_name: SP49-Sen_ibrutinib 10nM_48hr

value: ibrutinib 10nM


title: CML228.rep1

description:
ATAC
Genotype aggregated nuclei

tag: genotype


title: B97.rep1

description:
ATAC
Genotype aggregated nuclei


title: Donor_3_ATXN7L3_F1_ATAC


title: CML103.rep2

description:
ATAC
Genotype aggregated nuclei


title: SS.IB.1UM.48.2 [RNA-seq]


title: wat_32 (MI-24h)


title: Donor_3_AAVS1_8_D5_ATAC


title: SS.IB.1UM.48.1 [RNA-seq]


title: wat_25 (SHAM-24h)


title: Donor_3_AAVS1_7_D7_ATAC


title: wat_4 (MI-6h)


title: B73.rep4

description:
ATAC
Genotype aggregated nuclei


title: wat_37 (SHAM-6h)


title: SS.DMSO.6.3 [RNA-seq]

value: DMSO


title: wat_21 (SHAM-24h)


title: B73.rep2

description:
ATAC
Genotype aggregated nuclei


title: Donor_3_AAVS1_6_D12_ATAC


title: SS.DMSO.6.2 [RNA-seq]


title: Donor_3_AAVS1_5_E3_ATAC


title: B73.rep1

description:
ATAC
Genotype aggregated nuclei


title: wat_20 (MI-24h)


title: wat_19 (SHAM-24h)


title: SS.DMSO.6.1 [RNA-seq]


title: B97.rep2

description:
ATAC
Genotype aggregated nuclei


title: wat_17 (SHAM-24h)


title: Donor_3_AAVS1_3_E6_ATAC


title: Donor_3_AAVS1_2_C11_ATAC


title: Donor_3_AAVS1_1_E11_ATAC


title: maize_Ear_rep_1_H3K4me1

description: Chip sample

source_name: ear

value: ear

tag: chip antibody


title: SS.DMSO.48.2 [RNA-seq]


title: B73.rep3

description:
ATAC
Genotype aggregated nuclei

source_name: seedling


title: wat_16 (MI-24h)

tag: strain


title: wat_10 (MI-6h)


title: Donor_1_ZNF217_A6_ATAC

source_name: CD4+CD25- T cells


title: Donor_1_YY1_B2_ATAC


title: SIR.NVP2.20.6.3 [RNA-seq]

source_name: SP49-IR_NVP-2 20nM_6hr

value: resistant


title: muscle_7 (SHAM-6h)

source_name: muscle

value: muscle


title: muscle_5 (SHAM-6h)


title: Donor_1_TNFAIP3_A12_ATAC


title: SIR.NVP2.20.6.2 [RNA-seq]


title: pto_6h_10

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0

value: Pto

tag: host genotype

tag: replicate


title: pto_6h_12


title: mock_6h_11

value: mock


title: muscle_44 (MI-6h)


title: SIR.NVP2.20.6.1 [RNA-seq]

tag: cell line

tag: group


title: Donor_1_STAT5B_A10_ATAC


title: mock_6h_10


title: SS.DMSO.48.1 [RNA-seq]

tag: ibrutnib sensitivity

tag: treatment time


title: SS.DMSO.48.3 [RNA-seq]


title: muscle_41 (SHAM-6h)


title: SIR.NVP2.20.48.3 [RNA-seq]

source_name: SP49-IR_NVP-2 20nM_48hr


title: Donor_1_STAT5A_B3_ATAC


title: L148_6h_9

description:
L148_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: muscle_4 (MI-6h)


title: SIR.NVP2.20.48.2 [RNA-seq]


title: Donor_1_RELA_A2_ATAC


title: muscle_37 (SHAM-6h)


title: mock_6h_12


title: SIR.NVP2.20.48.1 [RNA-seq]


title: Donor_1_MYB_B1_ATAC


title: L70_6h_9

description:
L70_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: SIR.INC.500.48.3 [RNA-seq]


title: L58_6h_9

description:
L58_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: muscle_34 (MI-24h)


title: muscle_32 (MI-24h)


title: Donor_1_MED12_C1_ATAC


title: Donor_1_MBD2_C4_ATAC


title: SIR.INC.500.48.2 [RNA-seq]


title: Donor_1_KMT2A_C2_ATAC


title: L53_6h_9

description:
L53_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: muscle_25 (SHAM-24h)


title: L48_6h_9

description:
L48_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: SIR.INC.500.48.1 [RNA-seq]


title: muscle_21 (SHAM-24h)


title: mock_6h_9

description:
mock_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: SIR.IB.INC.48.3 [RNA-seq]


title: muscle_20 (MI-24h)


title: Donor_1_JAK3_B11_ATAC


title: L127_6h_9

description:
L127_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: SIR.IB.INC.48.2 [RNA-seq]


title: muscle_19 (SHAM-24h)


title: Donor_1_KLF2_A4_ATAC


title: L148_6h_8

description:
L148_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: SIR.IB.INC.48.1 [RNA-seq]


title: Donor_1_IRF2_B6_ATAC


title: muscle_16 (MI-24h)


title: L127_6h_8

description:
L127_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: L70_6h_8

description:
L70_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: SIR.IB.1UM.48.2 [RNA-seq]

source_name: SP49-IR_ibrutinib 10nM_48hr


title: SIR.IB.1UM.48.3 [RNA-seq]


title: muscle_10 (MI-6h)


title: L58_6h_8

description:
L58_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: Donor_1_IRF1_B12_ATAC


title: SIR.IB.1UM.48.1 [RNA-seq]


title: SIR.DMSO.6.3 [RNA-seq]


title: L53_6h_8

description:
L53_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: Donor_1_HIVEP2_B5_ATAC


title: liver_7 (SHAM-6h)

source_name: liver

value: liver


title: L48_6h_8

description:
L48_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: SIR.DMSO.6.2 [RNA-seq]


title: liver_5 (SHAM-6h)


title: liver_44 (MI-6h)


title: mock_6h_8

description:
mock_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: Donor_1_FOXP1_B8_ATAC


title: Donor_1_IRF4_C7_ATAC


title: muscle_17 (SHAM-24h)


title: SIR.DMSO.48.3 [RNA-seq]


title: SIR.DMSO.6.1 [RNA-seq]


title: L127_6h_7

description:
L127_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Donor_1_FOXK1_A8_ATAC


title: L148_6h_7

description:
L148_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: liver_42 (MI-6h)


title: SIR.DMSO.48.1 [RNA-seq]


title: liver_41 (SHAM-6h)


title: Donor_1_IL2RA_B9_ATAC


title: SIR.DMSO.48.2 [RNA-seq]


title: L70_6h_7

description:
L70_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Donor_1_CBFB_C8_ATAC


title: L58_6h_7

description:
L58_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Donor_1_GATA3_A5_ATAC


title: liver_4 (MI-6h)


title: Donor_1_ATXN7L3_C5_ATAC


title: L53_6h_7

description:
L53_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: liver_37 (SHAM-6h)


title: L48_6h_7

description:
L48_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: JS.NVP2.20.6.2 [RNA-seq]

source_name: Jeko-1-Sen_NVP-2 20nM_6hr


title: JS.NVP2.20.6.3 [RNA-seq]


title: Donor_1_AAVS1_8_A9_ATAC


title: JS.NVP2.20.6.1 [RNA-seq]


title: mock_6h_7

description:
mock_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: liver_35 (SHAM-6h)


title: Donor_1_AAVS1_7_A11_ATAC


title: JS.NVP2.20.48.3 [RNA-seq]

source_name: Jeko-1-Sen_NVP-2 20nM_48hr


title: Soil763_6h_6

description:
Soil763_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: liver_40 (MI-6h)


title: Donor_1_AAVS1_5_B7_ATAC


title: Root935_6h_6

description:
Root935_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: liver_34 (MI-24h)


title: Donor_1_ETS1_C6_ATAC


title: JS.NVP2.20.48.2 [RNA-seq]


title: liver_32 (MI-24h)


title: Donor_1_AAVS1_6_B4_ATAC


title: JS.NVP2.20.48.1 [RNA-seq]


title: liver_30 (MI-24h)


title: Root604_6h_6

description:
Root604_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: Donor_1_AAVS1_4_A1_ATAC


title: liver_25 (SHAM-24h)


title: Donor_1_AAVS1_3_B10_ATAC


title: JS.INC.500.48.3 [RNA-seq]


title: Root147_6h_6

description:
Root147_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: liver_21 (SHAM-24h)


title: Donor_1_AAVS1_2_A3_ATAC


title: JS.INC.500.48.1 [RNA-seq]


title: JS.INC.500.48.2 [RNA-seq]


title: Donor_1_AAVS1_1_C3_ATAC


title: Leaf177_6h_6

description:
Leaf177_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: liver_20 (MI-24h)


title: Leaf176_6h_6

description:
Leaf176_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: liver_17 (SHAM-24h)


title: Leaf1_6h_6

description:
Leaf1_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: mild symptomatic COVID-19 donor, 201657790 (VDJ)

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The single-cell from the BCR libraries were processed using Cell Ranger v4.0.0.
The command “cellranger vdj” was provided with reference file refdata-cellranger-vdj-GRCh38-alts-ensembl-4.0.0
Genome_build: hg38
Supplementary_files_format_and_content: The annotation for all high confidence cellular contigs

source_name: cryopreserved PBMCs

extract_protocol:
Cryopreserved PBMCs were thawed before being slowly transferred to a 50 ml conical tube and diluted in PBS containing 0.5 mM EDTA buffer (PEB). The cells were then centrifuged at 300 x g for 5 minutes at 4°C, washed twice and resuspended in 0.5 ml PEB. B cells were isolated from PBMCs by Human Pan B cell immunomagnetic negative selection kit (StemCell Technologies, MA) per manufacturer’s instructions. Cell concentration was determined using trypan blue staining with a TC20 automated cell counter (Biorad, CA) and adjusted if necessary, to achieve the desired concentration of 700-1200 cells/µl.
About 7,000 purified B-cells from each sample were combined with Chromium Next GEM Single Cell 5ʹ Gel Beads v1.1 and Reverse Transcription master mix (10x Genomics, CA) to generate barcoded Gel beads in emulsion (GEM) according to the manufacturer’s recommendations. The GEMs were recovered and purified using silane magnetic beads (Thermo Fisher Scientific, MA). The full-length cDNA along with cell-barcode identifiers were PCR amplified for 11 cycles and then purified using SPRISelect magnetic beads (Beckman Coulter, CA). The purified cDNA was inactivated in 80% ethanol before being removed from BSL-4. The quality of ethanol precipitated DNA was assessed by Bioanalyzer and both B-cell receptor (BCR) and 5’ gene expression (GEX) libraries were prepared as per manufacturer’s instructions. Libraries were quantified, both GEX and BCR libraries were pooled according to equivalent molar concentrations and sequenced on Illumina NovaSeq6000 sequencing platform.
BCR and 5'GEX

tag: disease state

value: mild symptomatic COVID-19

tag: Sex

value: F

tag: time

value: 31 days post symptom onset (DPSO)

value: PBMCs


title: liver_19 (SHAM-24h)

tag: age

tag: protocol

tag: time point


title: JS.IB.INC.48.2 [RNA-seq]

tag: cell type

value: Mantle cell lympohoma

value: sensitive


title: JS.IB.INC.48.3 [RNA-seq]

tag: treatment


title: JS.IB.INC.48.1 [RNA-seq]


title: mock_6h_6

description:
mock_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: Soil763_6h_5

description:
Soil763_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: mild symptomatic COVID-19 donor, 201657785 (VDJ)

value: 25 days post symptom onset (DPSO)


title: mild symptomatic COVID-19 donor, 201657787 (VDJ)

value: 37 days post symptom onset (DPSO)


title: liver_16 (MI-24h)

tag: tissue

value: 10 weeks

value: Myocardial infarction


title: Root935_6h_5

description:
Root935_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: mild symptomatic COVID-19 donor, 201657783 (VDJ)

value: M

value: 24 days post symptom onset (DPSO)


title: JS.IB.1UM.48.2 [RNA-seq]

source_name: Jeko-1-Sen_ibrutinib 1uM_48hr

value: ibrutinib 1uM


title: mild symptomatic COVID-19 donor, 201657037 (VDJ)

value: 27 days post symptom onset (DPSO)


title: heart_7 (SHAM-6h)

source_name: heart

value: heart

value: SHAM


title: Root604_6h_5

description:
Root604_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: JS.IB.1UM.48.1 [RNA-seq]


title: liver_10 (MI-6h)

value: liver


title: heart_5 (SHAM-6h)


title: mild symptomatic COVID-19 donor, 201657036 (VDJ)

value: mild symptomatic COVID-19

value: 33 days post symptom onset (DPSO)


title: mild symptomatic COVID-19 donor, 201657034 (VDJ)


title: heart_44 (MI-6h)


title: Root147_6h_5

description:
Root147_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: JS.DMSO.6.3 [RNA-seq]

value: DMSO


title: JS.DMSO.6.2 [RNA-seq]


title: liver_13 (SHAM-24h)


title: Leaf177_6h_5

description:
Leaf177_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: Leaf176_6h_5

description:
Leaf176_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: JS.IB.1UM.48.3 [RNA-seq]


title: heart_42 (MI-6h)


title: JS.DMSO.6.1 [RNA-seq]


title: Leaf1_6h_5

description:
Leaf1_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: Normal healthy donor, 2010113875 (VDJ)

value: Normal healthy

value: PBMCs


title: heart_41 (SHAM-6h)


title: Normal healthy donor, 2010113904 (VDJ)


title: heart_40 (MI-6h)


title: Soil763_6h_4

description:
Soil763_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Normal healthy donor, 2010113866 (VDJ)


title: heart_4 (MI-6h)


title: JS.DMSO.48.1 [RNA-seq]

value: Mantle cell lympohoma

value: sensitive


title: JS.DMSO.48.2 [RNA-seq]


title: mock_6h_5

description:
mock_6h_2
Arabidopsis thaliana Col-0
plant_count.txt

value: mock


title: heart_37 (SHAM-6h)

value: 10 weeks


title: JIR.NVP2.20.6.3 [RNA-seq]

source_name: Jeko-1-IR_NVP-2 20nM_6hr

value: resistant

value: NVP-2 20nM


title: mild symptomatic COVID-19 donor, 201657787 (GEX)

data_processing:
The single-cell from the 5’GEX libraries were processed using Cell Ranger v4.0.0.
The command “cellranger count” was provided with the reference refdata-gex-GRCh38-2020-A
Genome_build: hg38
Supplementary_files_format_and_content: hdf5 matrix file that contains the UMIs of all genes and all cells

value: F

value: 37 days post symptom onset (DPSO)


title: Root604_6h_4

description:
Root604_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: heart_35 (SHAM-6h)


title: JIR.NVP2.20.6.2 [RNA-seq]


title: Root147_6h_4

description:
Root147_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: mild symptomatic COVID-19 donor, 201657785 (GEX)

value: 25 days post symptom onset (DPSO)


title: heart_34 (MI-24h)

value: heart

value: Myocardial infarction


title: JIR.NVP2.20.6.1 [RNA-seq]


title: JS.DMSO.48.3 [RNA-seq]


title: Normal healthy donor, 2010113873 (VDJ)


title: heart_32 (MI-24h)


title: mild symptomatic COVID-19 donor, 201657037 (GEX)

value: 27 days post symptom onset (DPSO)


title: Leaf176_6h_4

description:
Leaf176_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: JIR.NVP2.20.48.3 [RNA-seq]

source_name: Jeko-1-IR_NVP-2 20nM_48hr


title: mild symptomatic COVID-19 donor, 201657036 (GEX)

value: mild symptomatic COVID-19

value: M


title: Leaf1_6h_4

description:
Leaf1_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: mild symptomatic COVID-19 donor, 201657790 (GEX)

value: 31 days post symptom onset (DPSO)


title: JIR.NVP2.20.48.1 [RNA-seq]


title: JIR.NVP2.20.48.2 [RNA-seq]


title: mild symptomatic COVID-19 donor, 201657034 (GEX)

value: 24 days post symptom onset (DPSO)


title: heart_25 (SHAM-24h)

value: SHAM


title: Root935_6h_4

description:
Root935_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: mock_6h_4

description:
mock_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: heart_21 (SHAM-24h)


title: Normal healthy donor, 2010113904 (GEX)

value: Normal healthy

value: PBMCs


title: mild symptomatic COVID-19 donor, 201657783 (GEX)


title: D36E_6h_3 TN_P_021

description:
D36E_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: R563_6h_3 TN_P_020

description:
R563_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: Leaf177_6h_4

description:
Leaf177_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: JIR.INC.500.48.1 [RNA-seq]

value: Mantle cell lympohoma


title: JIR.INC.500.48.3 [RNA-seq]


title: Normal healthy donor, 2010113873 (GEX)


title: L404_6h_3 TN_P_019

description:
L404_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: Normal healthy donor, 2010113875 (GEX)


title: heart_30 (MI-24h)

value: 10 weeks


title: heart_17 (SHAM-24h)


title: heart_20 (MI-24h)


title: JIR.IB.INC.48.3 [RNA-seq]

value: resistant


title: Normal healthy donor, 2010113866 (GEX)


title: L187_6h_3 TN_P_018

description:
L187_6h_3
Arabidopsis thaliana Col-0
plant_count.txt


title: JIR.IB.INC.48.2 [RNA-seq]


title: heart_16 (MI-24h)


title: ∆CAPH2 1 [Hi-C]

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: ∆CAPH2 replicate 2

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.9 (Servant et al., 2015).
Genome_build: hg19, hg38
Supplementary_files_format_and_content: Hi-C summary file (contains the genomic position and strand of the two pairs of a Hi-C ligation) and .hic file (contains contact matrices at various resolutions). The .aca.hic files are .hic files and contain the contact matrix resulting from an aggregrate chromosome analysis (ACA, see associated paper). Files 'hg19.no_centromere_gaps_CAPH2.aca.hic' and 'hg38_CAPH2.aca.hic': GSM4983062 and GSM4983063. Files 'hg19.no_centromere_gaps_wildtype.aca.hic' and 'hg38_wildtype.aca.hic' incorporate data from the samples listed previously published (GSM2494290, GSM2494294, and GSM2494298).

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Gibco) supplemented with 10% FBS (Sigma Aldrich), 1% Penicillin-Streptomycin (Gibco) and 1% L-Glutamine (Gibco). Cells were cultured at 37 degrees with 5% CO2.

extract_protocol:
Hi-C was performed as previously described (Rao et al. 2014), with slight modifications as described in (Haarhuis et al. 2017). Replicates were pooled after assessing their similarity.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

treatment_protocol: CAP-H2 knockout cells were obtained as described in (Elbatsh et al. 2019).

tag: genotype

value: delta CAPH2


title: L155_6h_3 TN_P_017

description:
L155_6h_3
Arabidopsis thaliana Col-0
plant_count.txt

tag: strain


title: JIR.IB.INC.48.1 [RNA-seq]


title: heart_13 (SHAM-24h)


title: JIR.IB.1UM.48.3 [RNA-seq]

source_name: Jeko-1-IR_ibrutinib 1uM_48hr

value: ibrutinib 1uM


title: JIR.INC.500.48.2 [RNA-seq]


title: L130_6h_3 TN_P_016

description:
L130_6h_3
Arabidopsis thaliana Col-0
plant_count.txt

tag: host genotype


title: heart_19 (SHAM-24h)


title: ∆CAPH2 2 [Hi-C]

description: ∆CAPH2 replicate 1


title: psoriasis3 10x scRNA-seq

city: Solna

first: Yizhou

last: Hu

state: Stockholm

address: C6 , Biomedicum Karolinska, Solnavägen 9,

institute: Karolinska Institute

description: 10x genomics (V3.1)

data_processing:
Count data were subsequently generated using CellRanger
10x demux pipeline was used to demultiplex the flowcells, and Fastq files were demultiplexed using mkfastq included in CellRanger.
Quality control of the processed expression matrix were performed by evaluating detected transcripts, detected counts, cell doublets, mito-ratio
Genome_build: GENCODE: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: HDF5 Loom file include raw counts, patient ID, UMAP, TSNE coordinates for each Sample

extract_protocol:
Surgical tissue samples were obtained in accordance with the protocol approved by regional ethical review board. Patients with definite diagnosis of psoriasis were selected as donors, and the full-thickness skin of the lesion was excised surgically, and donors without systemic diseases undergoing surgery were selected as healthy controls, whose normal skin around the surgical margin was taken for the study. Subcutaneous fat and soft tissue were carefully scraped off using a scalpel. The full-thickness skin of the donor's trunk, about 1cm2 in size, was removed by surgery then transported in PBS buffer at 4 ℃ for less than 30 minutes from cutting to dissociation. Samples digestion was performed using the whole skin dissociation kit for human (130-101-540, Miltenyi Biotec). Enzymatic digestion was completed in 2h, followed by mechanical dissociation using gentleMacs Dissociator running the gentleMACS program h_skin_01. The red blood cell lysate buffer (C3702, Beyotime) was used to decompose the suspension on ice at 4 ℃ for 20 minutes. The total number of cells and the ratio of living cells were calculated by microscopy with 0.4% trypan blue (C0040, Solarbio) staining. Single cell suspension with a cell count more than 500,000 and alive cell rate more than 90% observed under a microscope can be tested in the next step.
Full protocol according to 10x genomics (V3.1)

value: skin

value: psoriasis


title: mock_6h_3 TN_P_015

description:
mock_6h_3
Arabidopsis thaliana Col-0
plant_count.txt

value: mock

tag: replicate


title: ChIP-seq_input_ESCs_E2f6KO

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

data_processing:
Reads were cleaned to remove low quality bases and adapters with Trim Galore v0.4.4 using the parameters -q 20 -O 2 -a AGATCGGAAGAGC.
Reads were aligned to the mouse mm10 genome using bowtie2 and only reads mapping with a quality above 10 were kept using samtools.
Read density tracks were generated using genomeCoverageBed from Bedtools from reads extended to 200 bp (options -g mm10 -e 200).
Genome_build: mm10
Supplementary_files_format_and_content: We provide bigWig files for visualization of ChIP-seq tracks.
Supplementary_files_format_and_content: We provide bigWig files for visualization of RNA-seq tracks.
Supplementary_files_format_and_content: We provide IGV files containing methylation scores for all CGs with at least 5X sequencing depth.
Supplementary_files_format_and_content: We provide IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

source_name: ES cells

growth_protocol: ES cells were grown in Knockout DMEM with 10% Knockout Serum replacement, 5% fetal calf serum in the presence of LIF on gelatine coated plates.

extract_protocol:
ES Cells were crosslinked in PBS with 1% formaldehyde for 15 min on ice and quenched with 125 mM glycine for 5 min. Cells were lyzed and sonicated with a Bioruptor (Diagenode) at 4°C. ChIP was performed overnight at 4°C on 80 μg of chromatin with an anti-E2F6 antibody (ab53061, Abcam) pre-bound to Dynabeads protein G. The beads were washed and bound chromatin was eluted with elution-buffer (1% SDS, 0.1 M NaHCO3). Crosslinking was reverted at 62°C overnight in the presence of proteinase K (Qiagen) and DNA was purified with a PCR Purification Kit (Qiagen)
ChIP-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: developmental stage

tag: genetic background

tag: chip antibody


title: psoriasis2 10x scRNA-seq

description: 10x genomics (V3.1)


title: D36E_6h_2 TN_P_014

description:
D36E_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: JIR.IB.1UM.48.2 [RNA-seq]

tag: cell line

tag: group

tag: ibrutnib sensitivity

tag: treatment time


title: psoriasis1 10x scRNA-seq

description: 10x genomics (V3.1)

tag: disease state


title: JIR.IB.1UM.48.1 [RNA-seq]


title: ChIP-seq_E2F6_ESCs_E2f6KO


title: JIR.DMSO.6.3 [RNA-seq]

value: DMSO


title: R563_6h_2 TN_P_013

description:
R563_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: ChIP-seq_input_ESCs_WT

value: wild type


title: skin control3 10x scRNA-seq

description: 10x genomics (V3.1)

value: healthy


title: L404_6h_2 TN_P_012

description:
L404_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: L187_6h_2 TN_P_011

description:
L187_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: skin control2 10x scRNA-seq

description: 10x genomics (V3.1)


title: skin control1 10x scRNA-seq

description: 10x genomics (V3.1)


title: JIR.DMSO.6.2 [RNA-seq]


title: JIR.DMSO.6.1 [RNA-seq]


title: 21_Hakai_rep3

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

data_processing:
The libraries were sequenced on NextSeq500 with 85 bp paired end
The data was mapped agains Ensembl release 90 using STAR (v.2.5.1b).
Counts per gene were derived using featureCounts (v1.5.1)
Genome_build: BDGP6
Supplementary_files_format_and_content: counts per gene as tab separated file (tsv), read depth normalised bigwig tracks (bw)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: S2R+ cells

growth_protocol: S2R+ cells are maintained in Schenider Medium at room temperature

extract_protocol:
Cells were pelleted and RNA was isolated with Trizol using standart protocol
Librariesfor sequencing were prepared according to the NEBNext® Ultra™ Directional RNA Library Prep Kit protocol.

treatment_protocol: 3 dsRNA treatments (6 days total)

value: 10 ug of dsRNA against Hakai

tag: passages


title: L155_6h_2 TN_P_010

description:
L155_6h_2
Arabidopsis thaliana Col-0
plant_count.txt


title: 20_Hakai_rep2


title: JIR.DMSO.48.3 [RNA-seq]


title: heart_10 (MI-6h)

value: heart

tag: age

tag: protocol

value: Myocardial infarction

tag: time point


title: Amplicon_Plate_1_Donor_3_miniseq

data_processing:
Library strategy: Amplicon sequencing
Adapter sequences were trimmed from fastq files using cutadapt version 2.8 using default settings keeping a minimum read length of 50 bp. Insertions and deletions at each CRISPR target site were then calculated using Crispresso2 version 2.0.42 (Clement et al. 2019) with the following options "--quantification_window_size 3" and "--ignore_substitutions".
Genome_build: hg38
Supplementary_files_format_and_content: Modified amplicons

source_name: CD4+CD25- T cells

extract_protocol:
On day 5 (sgRNA #1 Donor 1-3) or day 7 (sgRNA #2 Donor 1, 3) post-electroporation, genomic DNA was isolated from each sample using DNA QuickExtract (Lucigen, Cat #QE09050) according to the manufacturer’s protocol.
Primers were designed to flank each sgRNA genomic target site. Amplicons containing CRISPR edit sites were generated by adding 1.25 µL each of forward and reverse primer at 10nM to 5 µL of sample in QuickExtract, 12.5 µL of NEBNext Ultra II Q5 master mix (NEB, Cat #M0544L), and H2O to a total 25 µL reaction volume. The following PCR cycling conditions were used: 98°C for 3 minutes, 15 cycles of 94°C for 20 seconds followed by 65°C-57.5°C for 20 seconds (0.5°C incremental decreases per cycle), and 72°C for 1 minute, and a subsequent 20 cycles at 94°C for 20 seconds, 58°C for 20 seconds and 72°C for 1 minute, and a final 10 minute extension at 72°C. Samples were then diluted 1:200 and subsequently Illumina sequencing adapters and indices were added in a second PCR reaction. Indexing reactions included 1 µL of the diluted PCR1 sample, 2.5 µL of each the forward and reverse indexing primers at 10 µM each, 12.5 µL of NEB Q5 master mix, and H2O to a total 25 µL reaction volume. The following PCR cycling conditions were used: 98°C for 30 seconds, followed by 98°C for 10 seconds, 60°C for 30 seconds, and 72°C for 30 seconds for 12 cycles, and a final extension period at 72°C for 2 minutes. Samples were quantified in a 96-well plate reader using the Quant-IT DNA high sensitivity assay kit (Invitrogen, Cat #Q33232) according to the manufacturer’s protocol and pooled into 1 tube. Post pooling, samples were then SPRI purified, and quantified using an Agilent 4200 TapeStation. Samples were then sequenced on an Illumina MiniSeq or NextSeq with PE 300 reads.

tag: cell type

value: CD4+CD25- T cells


title: 19_Hakai_rep1

tag: treatment


title: L130_6h_2 TN_P_009

description:
L130_6h_2
Arabidopsis thaliana Col-0
plant_count.txt

tag: strain


title: JIR.DMSO.48.2 [RNA-seq]


title: mock_6h_2 TN_P_008

description:
mock_6h_2
Arabidopsis thaliana Col-0
plant_count.txt

tag: host genotype


title: Amplicon_Plate_1_Donor_2_nextseq


title: 03_Ctr_rep3

value: 10 ug of dsRNA against LacZ

tag: replicate


title: JIR.DMSO.48.1 [RNA-seq]


title: Amplicon_Plate_1_Donor_2_miniseq


title: ChIP-seq_E2F6_ESCs_WT

tag: developmental stage

tag: genotype


title: 02_Ctr_rep2


title: Amplicon_Plate_1_Donor_1_miniseq


title: Soil763_col_3 TN_B_054

description:
Soil763_col_3
Actinobacteria
S763_combined.txt

organism: Arthrobacter sp. Soil763

source_name: Bacteria isolated from Arabidopsis thaliana


title: 01_Ctr_rep1


title: L404_6h_1 TN_P_005

description:
L404_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Amplicon_Plate_1_Donor_1_nextseq


title: R563_6h_1 TN_P_006

description:
R563_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Soil763_col_2 TN_B_035

description:
Soil763_col_2
Actinobacteria
S763_combined.txt


title: Soil763_col_1 TN_B_034

description:
Soil763_col_1
Actinobacteria
S763_combined.txt


title: Root935_col_3 TN_B_053

description:
Root935_col_3
Bacteroidetes
R935_combined.txt

organism: Flavobacterium sp. Root935


title: L187_6h_1 TN_P_004

description:
L187_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Activation screen, Library D+E, INPUT

city: Stanford

first: Adrian

middle: L

last: Sanborn

address: 299 Campus Drive West

institute: Stanford University

description: Plasmid library DNA

data_processing:
cutadapt 1.18 was used to discard reads without matching paired-end sublibrary sequencing primers and trim the primers in reads with matching primers
bwa-mem 0.7.17-r1188 was used to perform a first-pass alignment of reads to the DNA fragment library
Imperfectly mapped read pairs (i.e., those without paired read SAM flags of 99 and 147) were re-mapped to the library sequence with minimal edit distance
Supplementary_files_format_and_content: Excel file containing counts of reads aligned to each protein fragment

organism: Saccharomyces cerevisiae

source_name: Library D+E, INPUT

growth_protocol: S. cerevisiae strain BY4711 (ATCC 200873) was cultured in SC medium lacking tryptophan (SC-Trp)

extract_protocol:
Sorted cells were grown overnight and then pelleted. Pellets were treated with lyticase and then plasmid DNA was extracted using a Qiagen Miniprep kit.
The region of the plasmid encoding the variable protein fragment was PCR-amplified for 11-20 cycles (based on the OD600 of the culture) using Phusion polymerase with PCR primers that added flanking sequences corresponding to the standard Illumina sequencing primers. After a column cleanup, a second PCR was performed with primers that added sample-specific barcodes and the P5 and P7 sequences for Illumina sequencing.
OTHER:sequncing of designed plasmid library

treatment_protocol: overnight cultures were diluted to OD600 of 0.4 in SC-Trp-NAT-G418 with 10 nM beta-estradiol and grown for 4 hours at 30C before sorting on a BD Influx Cell Sorter

value: strain BY4711


title: Root935_vitro_3 TN_B_043

description:
Root935_vitro_3
Bacteroidetes
R935_combined.txt

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the  genome of corresponding commensal strain using Bowtie2 (version 2.2.8) with the parameters -p 20 -q --phred33 and transformed into a count per gene per library by using HTSeq (version 0.6.0).
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.


title: L155_6h_1 TN_P_003

description:
L155_6h_1
Arabidopsis thaliana Col-0
plant_count.txt

source_name: Arabidopsis thaliana Col-0


title: Activation screen, Library D+E, Bin 8

description: Plasmid library DNA

source_name: Library D+E, Bin 8


title: Activation screen, Library D+E, Bin 7

description: Plasmid library DNA

source_name: Library D+E, Bin 7


title: Root935_col_2 TN_B_033

description:
Root935_col_2
Bacteroidetes
R935_combined.txt


title: Soil763_vitro_2 TN_B_027

description:
Soil763_vitro_2
Actinobacteria
S763_combined.txt


title: L130_6h_1 TN_P_002

description:
L130_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Root935_col_1 TN_B_032

description:
Root935_col_1
Bacteroidetes
R935_combined.txt


title: Soil763_vitro_1 TN_B_026

description:
Soil763_vitro_1
Actinobacteria
S763_combined.txt


title: D36E_6h_1 TN_P_007

description:
D36E_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Activation screen, Library D+E, Bin 5

description: Plasmid library DNA

source_name: Library D+E, Bin 5


title: Soil763_vitro_3 TN_B_044

description:
Soil763_vitro_3
Actinobacteria
S763_combined.txt


title: mock_6h_1 TN_P_001

description:
mock_6h_1
Arabidopsis thaliana Col-0
plant_count.txt


title: Root935_vitro_2 TN_B_025

description:
Root935_vitro_2
Bacteroidetes
R935_combined.txt


title: Root935_vitro_1 TN_B_024

description:
Root935_vitro_1
Bacteroidetes
R935_combined.txt


title: Activation screen, Library D+E, Bin 3

description: Plasmid library DNA

source_name: Library D+E, Bin 3


title: Leaf155_vitro_3 TN_B_038

description:
Leaf155_vitro_3
Proteobacteria
L155_combined.txt

organism: Rhizobium sp. Leaf155


title: Leaf155_col_2 TN_B_045

description:
Leaf155_col_2
Proteobacteria
L155_combined.txt


title: Activation screen, Library D+E, Bin 6

description: Plasmid library DNA

source_name: Library D+E, Bin 6


title: Leaf176_col_2 TN_B_047

description:
Leaf176_col_2
Bacteroidetes
L176_combined.txt

organism: Pedobacter sp. Leaf176


title: Leaf155_vitro_1 TN_B_014

description:
Leaf155_vitro_1
Proteobacteria
L155_combined.txt


title: Activation screen, Library A+B, INPUT

description: Plasmid library DNA

source_name: Library A+B, INPUT


title: Activation screen, Library A+B, Bin 7

description: Plasmid library DNA

source_name: Library A+B, Bin 7


title: Leaf155_col_1 TN_B_003

description:
Leaf155_col_1
Proteobacteria
L155_combined.txt


title: Activation screen, Library A+B, Bin 8

description: Plasmid library DNA

source_name: Library A+B, Bin 8


title: Activation screen, Library D+E, Bin 1

description: Plasmid library DNA

source_name: Library D+E, Bin 1


title: Activation screen, Library A+B, Bin 6

description: Plasmid library DNA

source_name: Library A+B, Bin 6


title: Leaf1_vitro_3 TN_B_036

description:
Leaf1_vitro_3
Actinobacteria
L1_combined.txt

organism: Plantibacter sp. Leaf1


title: Leaf176_col_1 TN_B_004

description:
Leaf176_col_1
Bacteroidetes
L176_combined.txt


title: Leaf176_vitro_1 TN_B_016

description:
Leaf176_vitro_1
Bacteroidetes
L176_combined.txt


title: Activation screen, Library D+E, Bin 4

description: Plasmid library DNA

source_name: Library D+E, Bin 4


title: Activation screen, Library A+B, Bin 5

description: Plasmid library DNA

source_name: Library A+B, Bin 5


title: Leaf155_vitro_2 TN_B_015

description:
Leaf155_vitro_2
Proteobacteria
L155_combined.txt


title: Leaf176_col_3 TN_B_048

description:
Leaf176_col_3
Bacteroidetes
L176_combined.txt


title: Leaf1_vitro_1 TN_B_010

description:
Leaf1_vitro_1
Actinobacteria
L1_combined.txt


title: Activation screen, Library A+B, Bin 4

description: Plasmid library DNA

source_name: Library A+B, Bin 4


title: Activation screen, Library A+B, Bin 3

description: Plasmid library DNA

source_name: Library A+B, Bin 3


title: Leaf176_vitro_2 TN_B_017

description:
Leaf176_vitro_2
Bacteroidetes
L176_combined.txt

source_name: Bacteria isolated from Arabidopsis thaliana


title: Leaf1_col_3 TN_B_006

description:
Leaf1_col_3
Actinobacteria
L1_combined.txt


title: Activation screen, Library A+B, Bin 2

description: Plasmid library DNA

source_name: Library A+B, Bin 2


title: Leaf1_col_2 TN_B_002

description:
Leaf1_col_2
Actinobacteria
L1_combined.txt


title: Zebrafish pex2-/- 5wk pool of 3 rep4

type: RNA

city: Gifu city

first: Shigeo

last: Takashima

state: Gifu

address: 1-1 Yanagido

department: Life Science Research Center

country: Japan

institute: Gifu University

hyb_protocol: Hybridization was performed at 65 digrees C for 17h.

scan_protocol: The microarray slide was scanned with ArrayScan (Agilent).

data_processing: The signal was processed for digitization using Feature Extraction software (Agilent), and analyzed with GeneSpring GX software (Agilent) . Raw data were normalized by 75 percentile shift. Moderated t-test with Benjamini-Hochberg multiple testing correction was used to reveal the significant differences of gene expression. Corrected p-value cutoff of 0.05 was applied.

organism: Danio rerio

source_name: Equal amout of total RNA was mixed from 3 mutant larvae (pex2-/- siblings)

label_protocol: Cy3-labelled probes were prepared from RNA using Low Input Quick Amp Labeling Kit 1-color (Agilent Technologies, #5190-2305).

growth_protocol: Fish were raised with normal protocol.

extract_protocol: Total RNA was isolated from whole bodies of 5-week old mutant fish and their wild-type siblings using Maxwell RSC simplyRNA Tissue Kit (Promega, #AS1340) .

treatment_protocol: The genotype of the fish was determined using genome DNA extracted from a piece of tail fin.

value: Mutant siblings of pex2 typeC allele

tag: tissue

value: larvae

value: 5 weeks post fertilization


title: Leaf1_col_1 TN_B_001

description:
Leaf1_col_1
Actinobacteria
L1_combined.txt


title: Zebrafish pex2-/- 5wk pool of 3 rep2


title: Zebrafish pex2+/+ 5wk pool of 3 rep4

source_name: Equal amout of total RNA was mixed from 3 wild-type larvae (pex2+/+ siblings)

value: wild-type siblings of pex2 typeC allele


title: Zebrafish pex2-/- 5wk pool of 3 rep3


title: Zebrafish pex2+/+ 5wk pool of 3 rep3


title: Zebrafish pex2-/- 5wk pool of 3 rep1


title: Ago2.KO_oocytes.rep2

status: Public on Apr 25 2021

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

description:
LACE-seq
Ago2.KO_oocytes.bigwig

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After sequencing of LACE-seq libraries, the adapter sequences and the polyA tails at the 3' end were removed sequentially using Cutadapt v1.15 with the following two parameters: -f fastq -q 30,0 -a ATCTCGTATGCCGTCTTCTGCTT -m 18 --max-n 0.25 --trim-n, and -f fastq -a A{15} -m 18 -n 2.
After filtering, the LACE-seq reads were first aligned to human or mouse pre-rRNA by bowtie with default parameters, and the remaining unmapped reads were then aligned to the hg19 or mm9 reference genome. For LACE-seq data mapping, two mismatches and at most 10 multiple hits were allowed (bowtie parameters: -v 2 -m 10 --best --strata).
Genome_build: hg19 (GRCh37), mm9 (MGSCv37)
Supplementary_files_format_and_content: BigWig files were generated using bedtools genomecov v2.28.0 and bedGraphToBigWig v4 software.

source_name: Mouse Oocytes

growth_protocol: HeLa cells were cultured in DMEM containing 10% fetal bovine serum plus 100 U penicillin/streptomycin at 37°C in 5% CO2. K562 cells were cultured in RPMI-1640 containing 10% fetal bovine serum plus 100 U penicillin/streptomycin at 37°C in 5% CO2.

extract_protocol: After UV-C irradiation, RNA cross-linked to protein is purified and ligated with an adenylated DNA linker at the 3’end. Next, cDNA fragments, which stop exactly at the cross-link site in RNA, are generated through reverse transcription (RT), followed by polyadenylation, in vitro transcription (IVT), PCR amplification and high-throughput sequencing.

treatment_protocol: Female mice at six- to eight-weeks-old were injected with 10 IU of Pregnant Mare Serum Gonadotropin (PMSG) for 48 h. Meiosis II oocytes were collected 13 hour post human chorionic gonadotropin (hCG) injection from females previously primed with PMSG.

tag: genotype/variation

value: Ago2 cKO

tag: Sex

value: Female

value: MII oocytes

value: No treatment

tag: antibody

value: anti-Ago2 (Abcam, ab186733)


title: Ago2.WT_oocytes.rep1

description:
LACE-seq
Ago2.WT_oocytes.bigwig

value: Wild type


title: Ago2.KO_oocytes.rep1

description:
LACE-seq
Ago2.KO_oocytes.bigwig


title: Zebrafish pex2+/+ 5wk pool of 3 rep2


title: Ago2.50_oocytes.rep1

description:
LACE-seq
Ago2.50_oocytes.bigwig


title: Leaf1_vitro_2 TN_B_011

description:
Leaf1_vitro_2
Actinobacteria
L1_combined.txt


title: Control D8 replicate 3

city: Charlottesville

first: Bernard

middle: Victor

last: Thisse

state: VA

address: 1340 Jefferson Park ave

department: Cell Biology

institute: University of Virginia

data_processing:
Sequenced read were trimmed for adaptor sequences then mapped to UCSC mm10 whole genome using STAR 2.6.1a and indexed with samtools 0.1.20
Quantitation of reads aligning to each gene was done using featureCounts
DESeq2 Bioconductor package was used to normalize count data, estimate dispersion, and fit a negative binomial model for each gene.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: The processed data files contains the normalized counts for each genes in all 12 analyzed samples.

source_name: E14TG2a embryonic stem cells line

growth_protocol: Mouse embryonic stem cells (E14TG2a cell line) were cultivated in Knock-Out DMEM supplemented with 15% Serum Replacement, 3 uM Chir99021, 1 uM PD03259021, ESGRO LIF (1000 U/mL), L-glutamine, non-essential amino acids, beta-mercaptoethanol and antibiotic-antimycotic for 2 days at 37°C and 5% CO2. Aggregates of 50 cells and 100 cells (=embryoid bodies, EBs) were generated in hanging drops (Day 0 - D0) . EBs were transferred into  DMEM/F12 and Neurobasal Medium, supplemented with N2, B27, beta-mercaptoethanol and antibiotic-antimycotic, in hanging drops for 48 hours.

extract_protocol:
For each sample total RNA from pools of 12 embryoids were extracted with Qiagen Rneasy micro kit ( Qiagen#74004)
Libraries were constructed using NEB DNA Ultra library construction kit, with standard TruSeq-type adapters. Libraries size and concentration were assessed using Agilent 2,100 Bioanalyzer. Libraries were multiplexed and 75bp single-end were sequenced on illumina Nextseq 500

treatment_protocol: On Day 3, EBs of 50 cells were incubated in 10ng/ml of BMP4 for 8 hours. These BMP4 stimulated EBs were then merged to untreated EBs of 100 cells resulting in development of embryoids that were  cultured until day 7 or day 8 for RNA extraction. As control, two untreated EBs of 50 cells and 100 cells were merged at D3, cultured until D7 or D8 and treated as the embryoids for RNA analysis .

value: control

tag: cell line

tag: Stage


title: Embryoid D8 replicate 2

value: embryoid


title: Ago2.WT_oocytes.rep2

description:
LACE-seq
Ago2.WT_oocytes.bigwig


title: Embryoid D8 replicate 3


title: Control D8 replicate 2


title: Embryoid D7 replicate 3


title: Embryoid D8 replicate 1


title: Control D8 replicate 1


title: Embryoid D7 replicate 2


title: Activation screen, Library A+B, Bin 1

description: Plasmid library DNA

source_name: Library A+B, Bin 1


title: Zebrafish pex2+/+ 5wk pool of 3 rep1


title: Ago2.50_oocytes.withoutIVT.rep2

description:
LACE-seq
Ago2.50_oocytes.withoutIVT.bigwig


title: Ago2.50_oocytes.withoutIVT.rep1


title: Control D7 replicate 3


title: Embryoid D7 replicate 1


title: Control D7 replicate 2


title: Control D7 replicate 1