title: HEL_Ctrl_PRO-seq

city: Shang Hai

first: Zimei

last: Yang

address: Dongchuan road 800

institute: Shang Hai Jiaotong University

description: cell transducted by Control shRNA

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Reads were aligned using bowtie2 v2.3.4.1.
Low-quality alignments were filtered out using SAMtools (version 0.1.19) with command “samtools view -F 4 -q 10”. Strand-specific meta-gene profiles were generated using the groHMM package from Bioconductor. Strand-specific read coverage was calculated using “bedtools genomecov” with “-ibam”, “-bg” and “-strand” options and normalized by total mapped reads before loading to IGV for visualization.
hg38
BigWig files contains normalized read count

source_name: HEL

growth_protocol: Nascent RNA was extracted using Trizol and precipitated in 75% ethanol.

extract_protocol: Extracted nascent RNA was fragmented by base hydrolysis in 0.2 N NaOH on ice for 10~12 min, and neutralized by adding 1× volume of 1 M Tris-HCl pH 6.8. For PRO-cap, the fragmentation step was omitted. Excessive salt and residual NTPs were removed by using P-30 column (Bio-rad). Fragmented nascent RNA was bound to 30 µl of Streptavidin M-280 magnetic beads (Invitrogen) following the manufacturer’s instructions. The beads were washed once in high salt (2 M NaCl, 50 mM TrisHCl pH 7.4, 0.5% Triton X-100), once in medium salt (300 mM NaCl, 10 mM Tris-HCl pH 7.4, 0.1% Triton X-100), and once in low salt (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100). Bound RNA was extracted from the bead using Trizol (Invitrogen) in two consecutive extractions, and the RNA fractions were pooled, followed by ethanol precipitation. For the first ligation reaction, fragmented nascent RNA was redissolved in H2O and incubated with 10 pmol of reverse 3’ RNA adaptor and T4 RNA ligase I (NEB) under manufacturer’s condition for 6hr at 20˚C. For PRO-cap, the standard 3’ RNA adaptor (Illumina) was used. Ligated RNA was enriched with biotin-labeled products by another round of Streptavidin bead binding and extraction. To repair 5’ ends, the RNA products were treated with Tobacco Acid Pyrophosphatase (TAP, Epicentre) and Polynucleotide Kinase (PNK, NEB). Each reaction was followed by an ethanol precipitation step. For PRO-cap, PNK treatment step was omitted, and Antarctic phosphatase (AP, NEB) was used to treat the RNA preparation prior to TAP treatment to enrich for 5’ capped RNA. Since these procedures repair 5’ ends after the 3’ ligation, selfcircularized products were not expected during the first ligation step. 5’ repaired RNA was ligated to reverse 5’ RNA adaptor (5'-rCrUrGrArArCrArArGrCrArGrArArGrArCrGrGrCrArUrArCrGrA-3' or 5'-rCrCrUrUrGrGrCrArCrCrCrGrArGrArArUrUrCrCrA-3’ for using TruSeq barcodes (Illumina)). Standard 5’ RNA adaptors were used for PRO-cap. Ligated RNA products were further enriched for biotin-labels by the third round of streptavidin bead binding and extraction. Adaptor ligated nascent RNA was reverse transcribed using 25  pmol RT primer (5’-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA3’(GX2 primer, Illumina) or 5’- AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’ for TRU-seq barcodes (RP1 primer, Illumina). Standard Illumina RT primers were used for PRO-cap. A portion of the RT product was removed and used for trial amplifications to determine the optimal number of PCR cycles. For the final amplification, 12.5 pmol of GX1 primer (Illumina) or RPI-index primers (for TRU-seq barcodes, Illumina) was added to the RT product with Phusion polymerase (NEB) under standard PCR condition. Excess RT primer served as one primer of the pair used for the PCR. The product was amplified 12~18 cycles and PAGE purified before being analyzed by Illumina’s GenomeAnalyzer 2 or HiSeq 2000 machines.

value: HEL

value: Human erythroblast


title: HEL_AF9KD_PRO-seq

status: Public on Jul 15 2024

type: SRA

country: China

description: cell transducted by AF9 shRNA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: yb2 yb3 mutant leaves,B. cinerea infection, rep1

city: Hangzhou

first: Chuyu

last: Lin

state: Zhejiang

address: 866#, Yuhangtang Road

department: College of Agriculture and Biotechnology

institute: Zhejiang University

data_processing:
Reads were mapped to the Arabidopsis thaliana (TAIR10) genome using Hisat2 (version 2.1.0) with default settings.
Transcripts assembled from three independent biological replicates were included in the analysis, compared using DESeq2 (version 1.30.1) with default settings.
The R package DESeq2 (version 1.30.1) in v4.0.3 was employed to identify differentially expressed genes with at least a 1.5-fold change
Assembly: TAIR10
Supplementary files format and content: text files include genecounts for each files

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: The stratified seeds were germinated in half-strength Murashige and Skoog (MS) medium for 7 d and transferred to soil. Plants were grown under cool white light in a long-day condition (16 h light /8 h dark, 22 ºC).

extract_protocol:
Total RNA was extracted from 10-d-old seedlings using TRIzol reagent (Invitrogen, USA) and reverse-transcribed into cDNAs using commercial kits (TOYOBO, FSQ-301) following the manufacturer's instruction. Real-time PCR was performed using SYBR Green qPCR Master Mix (TOYOBO, QST-100) on the LightCycler480 system (Roche). The constitutively reference genes were used as the endogenous control to normalize the amount of cDNA templates.
RNA sequencing was carried out using the Illumina NovaSeq 6000 with Hiseq-PE150 strategy, conducted by Novogene Corporation (Beijing, China).

treatment_protocol: Four-week-old plants were infected by deposit a 5µl droplet of conidiophores suspension (2.5×106conidiophores/mL) on one side of the midvein or by spray inoculation with conidiophores suspension (2.5×106 conidiophores/mL) on the entire plant. The inoculated plants were covered with a transparent plastic lid to maintain high humidity.

tag: tissue

value: leaves

tag: genotype

value: yb2 yb3 mutant

tag: treatment

value: B. cinerea infection


title: yb2 yb3 mutant leaves,mock, rep2

value: Mock


title: yb2 yb3 mutant leaves,mock, rep3


title: yb2 yb3 mutant leaves,B. cinerea infection, rep3


title: yb2 yb3 mutant leaves,mock, rep1


title: Vh-WT-Rep1T

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street, Biology Building

department: Biology

country: USA

institute: Indiana University

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX)
Fastq to fasta conversion (FastX)
PolyA clipping (READemption 0.3.0)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.0)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.0)
Genome_build: CP000789.1, CP000790.1, CP000791.1
Supplementary_files_format_and_content: wiggle

organism: Vibrio campbellii

source_name: Bacterial lysate

growth_protocol: Cells were grown at 30°C in LM media to an OD600 of 1.0

extract_protocol:
Trizol Reagent followed by Dnase I treatment
For Illumina sequencing  of cDNA molecules, the libraries were constructed by vertis Biotechnology AG, Germany. The cDNA libraries were sequenced using a NextSeq 500 machine (Illumina) in single-read mode

treatment_protocol: When indicated samples were treated with Terminator Exonucleae (TEX; epicentre)

tag: strain

tag: agent

value: Terminator Exonucleae


title: yb2 yb3 mutant leaves,B. cinerea infection, rep2


title: WT leaves,B. cinerea infection, rep1

value: WT


title: Vh-luxR-Rep2T

value: deltaluxR (KM669)


title: WT leaves,mock, rep3


title: WT leaves,B. cinerea infection, rep3


title: WT leaves,mock, rep2


title: M263 cells,H3K27ac

city: Los Angeles

first: Xiang

last: Lu

state: CA

address: 10833 Le Conte Ave

department: Department of Molecular and Medical Pharmaacology

institute: University of California, Los Angeles

library_source: genomic

data_processing:
For ChIP-seq,Reads were mapped to the human genome hg19 by bowtie273. The identical aligned reads were deduplicated to avoid PCR duplicates. Peaks were called on the merged set of all ChIP-seq reads of M397 using MACS2 with the following parameters: --nomodel, --broad74.To visualize peaks in each sample, bed graph file was generated using MACS2 with following parametes: --nomodel, --broad, --bdg, --SPMR. For RNA-seq,Reads were aligned against the human genome (hg19) using STAR (v2.7.3a). Read counts were quantified using htseq-count with known gene annotations from UCSC.The gene expression level was calculated from Fragments Per Kilobase per Million reads (FPKM) normalized expression values
Assembly: hg19
Supplementary files format and content: bdg file includes peak file for each sample

molecule: genomic DNA

growth_protocol: M-series patient derived cell lines used in this study were generated under UCLA institutional review board approval # 11–003254. Cells were cultured in a water-saturated incubator at 37 °C with 5% CO2 in RPMI 1640 with L-glutamine (Life Technologies), supplemented with 10% fetal bovine serum (Omega), and 0.2% antibiotics (MycoZapTM Plus-CL from Lonza). The cell lines were tested for mycoplasma and were periodically authenticated to its early passage using GenePrint 10 System (Promega).HCC827(Cat.CRL-2868) and HT-29(Cat.HTB-38) were brought from ATCC. Cells were cultured in a water-saturated incubator at 37 °C with 5% CO2.

extract_protocol:
Briefly, cells were cultured to ~80% confluency in a petri dish containing 10 mL of growth media, and then fixed in 1% formaldehyde by adding 275 μl of 37% formaldehyde for 10 minutes to cross-link protein–DNA complexes at room temperature. The unreacted formaldehyde was quenched by adding Glycine to a final concentration 0.125 M. Gently swirl dish to mix. The nuclear pellet was isolated with Cell Lysis Buffer. The pellet was resuspended with 500 μl SDS Lysis Buffer containing 1X Protease Inhibitor Cocktail II before sonication for 4 min (10 s on, 30 s off, 10% strength in a Bioruptor to yield DNA fragments of 0.2-1.0 kb in length. The lysates were cleared by centrifugation (12,000g for 10 min at 4 °C) and diluted tenfold in ChIP dilution buffer to decrease the concentration of SDS. After keeping 10% of the sample as input, 500 μl supernatant was incubated overnight at 4 °C with antibody and 20 μL of fully resuspended protein A/G magnetic beads. The washing, elution, reverse cross-linking, and purification steps were performed according to manufacturer’s description. ChIPed Eluted DNA was quantified by Qubit dsDNA HS Assay Kit.Total RNA was extracted from the cell pellets using AllPrep DNA/RNA kit (Qiagen)
ChIP-seq libraries were prepared with Kapa DNA HyperPrep Kit (Kapa, Cat KK 8700) according to the manufacturer's protocol. Briefly, 5-10 ng of immunoprecipitated DNA was underwent end-repaired, A tailing and adaptor ligation. A 10 cycles of PCR was performed to produce the final sequencing library. As for ATAC, the Tn5 treated DNA was amplified with a 5-cycle PCR in 50µl reaction volume. The tubes were removed from thermocycler and used 5 µl of partially amplified library to perform qPCR to determine how many additional PCR cycles were needed. For the samples in this study, an additional 4-5 cycles of PCR was performed on the remaining 45ul of each partially amplified product. 1.8X AmpurXP beads purification was used for the final PCR cleanup. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit, and quantified with qPCR. For RNA-seq, sequencing libraries were prepared with TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, USA) with minor modifications.mRNA library was constructed with TruSeq RNA Sample Preparation Kit and sequenced on the Illumina Hiseq 2500 with pair-end 150bp reads following the manufacturer's recommendations by Novogene.

treatment_protocol: BRAF inhibitor (vemurafenib) from Selleck Chemicals LLC, were dissolved in DMSO at designated concentrations before applying to cell culture media. Cells were plated in 10cm tissue culture plate at 60% confluency and treated with certain drugs for the specified numbers of days. M397 cells were treated with 3uM of vemurafenib for 59days and at day29, drug were removed and cells were cultured with normal medium for another 35days.HCC827 cells were cultured using ATCC-formulated RPMI-1640 Medium (ATCC 30-2001) and treated with an EGFR inhibitor (erlotinib, SellecChem S1023).ATCC-formulated McCoy's 5a Medium Modified (ATCC 30-2007) was used to culture HT-29 cells and the cells were treated with an anti-EGFR antibody  (Cetuximab, SellecChem A2000) plus a BRAF inhibitor (Dabrafenib, MCE HY-14660)

value: melanoma cancer cell line

value: untreated


title: YB2-FLAG, anti-FLAG, rep2

data_processing:
The clean paired-end reads were mapped to the reference genome by Bowtie2 (Version 2.3.5) and reads with low mapping quality or multiple positions on the genome were identified and removed by SAMtools (version 1.9). Only perfectly and uniquely mapped reads were retained for further analysis.
Enriched peaks were called and annotated by MACS2 (Version 2.2.8) with the following parameters: “-f BAMPE -g 119145879 -q 0.01”. Peaks that were consistently found in two replicates were selected for further analyses. The generated data were imported into the Integrative Genomics Viewer (IGV) (James T Robinson, 2011) for visualization.
ComputeMatrix, plotProfile and plotHeatmap programs in deepTools (version 3.3.0) were used to compare the average enrichment at defined loci between YB2-FLAG and WT. To assign peaks to proximal genes, regions within 1.0 kb flanking the transcription start site (TSS) were extracted.
Assembly: TAIR10
Supplementary files format and content: bedGraph files generated from SAMtools
Supplementary files format and content: peak files generated from MACS2

extract_protocol:
Briefly, about 0.5-g 10-d-old seedlings were crosslinked with 1% formaldehyde and stopped with 125 mM glycine. Samples were ground and resuspended in the nuclei isolating buffer (10 mM Tris pH 8.0, 10 mM Sodium butyrate, 400 mM Sucrose, 0.1 mM PMSF, 5 mM β-mercaptoethanol, 1×cocktail protein inhibitor freshly). The isolated nuclei were resuspended with 1 mL lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM Sodium butyrate, 0.1% deoxycholate, 0.1% SDS, 1% Triton X-100, 1 mM PMSF and 1×protease inhibitor cocktail freshly) and sonicated into 200-500 bp fragments by Diagenode Bioruptor (high setting, 18 cycles，30s on and 30s off). Subsequently, the sonicated chromatin was incubated with anti-Flag M2 magnetic beads (Sigma, M8823) overnight at 4°C.
The recovered DNAs in ChIP assay were used to library construction with the Scale ssDNA-seq Lib Prep Kit (ABclonal, RK20228). High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China).

tag: chip antibody


title: WT leaves,mock, rep1


title: M381 cells,H3K4me3


title: WT leaves,B. cinerea infection, rep2


title: YB2-FLAG, anti-FLAG, rep1

value: anti-Flag M2 magnetic beads (Sigma, M8823)


title: Vh-luxR-Rep2


title: mice cecal content,F rep4

city: Ann Arbor

first: Keerthikka

last: Ravi

state: Michigan

address: 1105 N University st

department: Molecular, Cellular and Developmental Biology

institute: University of Michigan

description:
invivo_raw_counts.txt, S4
htseq count file
invivo_raw_counts.txt

data_processing:
The sequencing quality of RNA reads was first assessed using FatsQC, version 0.11.8.
TrimGalore, version 0.6.7, was used to trim out adapter reads, as well as remove reads smaller than 90bp.
The reads were aligned to the L. johnsonii MR1 using Bowtie2 version 2.3.4.3 with default parameters for an end-to-end alignment. The resulting SAM files were converted to BAM files using SAMtools version 1.7.
The count matrix was generated using HtSeq, version 0.12.4, and counts were imported to R for differential gene expression analysis.
FPKM reads were generated, and differentially expressed genes were identified using DESeq2.
Assembly: L. johnsonii MR1 was used as the reference CP091981.1
Supplementary files format and content: tab-limited text file includes raw counts for each sample condition

organism: Lactobacillus johnsonii

source_name: cecal content of  monocolonied Balb/c mice

growth_protocol: L. johnsonii MR1 was grown over night anaerobically at 37 °Cs. For the in vitro samples, cells were subcultured the next day, grown anaerobically at 37 °Cs, and collected at exponential (5 hrs) and stationary phase (10hr) for RNA seq.

extract_protocol:
For the in vitro samples, protease treament followed by RNA isolation was performed as per the bacterial RNA isolation protocol from Qiagen Rneasy Kit. For the in vivo samples, Trizol/Rneasy hybrid protocol by Mauricio Rodriguez-Lanetty was followed.
NEBNext Ultra II DNA library prep was used for cDNA library preperation.
RNA-seq. Sequencing was done using Novoseq, paired-end sequencing, with a sequencing depth of 33M reads per sample for in vitro samples and 150M reads per sample for in vivo samples.

treatment_protocol: For the in vitro transcriptomics, gnotobiotic  Balb/c mice (F=8, M=2) were orally gavaged with 10^8 CFU of L. johnsonii MR1, grown over night under anaerobic conditions at 37 °C. Seven days after the oral gavage, the the cecal contents of the mice was harvest for in vivo bacterial transcriptomic analysis.

value: Prokaryotic


title: mice cecal content,M rep5

description:
invivo_raw_counts.txt, S5
htseq count file
invivo_raw_counts.txt

value: cecal content of  monocolonied Balb/c mice


title: mice cecal content,F rep6

description:
invivo_raw_counts.txt, S6
htseq count file
invivo_raw_counts.txt


title: mice cecal content,F rep8

description:
invivo_raw_counts.txt, S8
htseq count file
invivo_raw_counts.txt


title: mice cecal content,F rep2

description:
invivo_raw_counts.txt, S2
htseq count file
invivo_raw_counts.txt


title: Anaerobic stationary phase rep3

description:
invitro_stationary_phase_raw_counts.txt, column S3
htseq count file
invitro_stationary_phase_raw_counts.txt

source_name: 10hr anaerobic culture

value: 10hr anaerobic culture


title: Anaerobic exponential phase rep1

description:
invitro_exponential_phase_raw_counts.txt, S1
htseq count file
invitro_exponential_phase_raw_counts.txt

source_name: 5hr anaerobic culture

value: 5hr anaerobic culture


title: Anaerobic stationary phase rep2

description:
invitro_stationary_phase_raw_counts.txt, column S2
htseq count file
invitro_stationary_phase_raw_counts.txt


title: Anaerobic exponential phase rep2

description:
invitro_exponential_phase_raw_counts.txt, S2
htseq count file
invitro_exponential_phase_raw_counts.txt


title: YB2-FLAG, input


title: mice cecal content,F rep3

description:
invivo_raw_counts.txt, S3
htseq count file
invivo_raw_counts.txt


title: mice cecal content,F rep1

description:
invivo_raw_counts.txt, S1
htseq count file
invivo_raw_counts.txt


title: RNAseq_Aapp_Isolate9183

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Enzymatic Methyl-seq: All reads were filtered and trimmed with fastp using default parameters. Then the trimmed reads mapped to the reference genome (including a lambda phage and pUC19 sequences as negative and positive controls) using BS-Seeker2 backed with bowtie2. Sambamba (markdup) was used to remove PCR duplicates and CGmapTools was used to obtain the methyl calls, resulting in the CGmap files in this repository. More information on this file format here: https://github.com/BSSeeker/BSseeker2.
RNA-seq: All reads were filtered and trimmed with fastp. To obtain TPMs, we used Kallisto (0.46) against the reference mRNA annotation using default parameters. To obtain a counts file we first used HISAT2 allowing multimapping reads, and then used the TElocal pipeline to obtain counts from the bam files. De novo transcriptome assemblies were obtained using Trinity-v2.8.5 using stranded information and the jaccard_clip option.
Assembly: For all the Amoebidium appalachense experiments, the data was mapped to the reference genome that can be found in ENA number ERZ21989579. Sphaerforma assembly is found here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_008580545.1/. Creolimax fragrantissima assembly is found here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002024145.1/. Chromosphaera perkinsii genome can be found here: https://figshare.com/articles/dataset/Genome_-_Chromosphaera_perkinsii/5426494.
Supplementary files format and content: CGmap files are the direct output from CGmapTools / BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain:  (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C /
Supplementary files format and content: Counts / TPM matrixes contain the reads count obtained from the TEcount pipeline (https://github.com/bodegalab/tecount) or the TPMs obtained from Kallisto. Trinity fasta files are the de novo transcriptome assembly for each RNA-seq library.

molecule: polyA RNA

organism: Amoebidium appalachense

growth_protocol: Amoebidium isolates were grown on Brain Heart Infusion (10% BHI, ThermoFisher CM1135) liquid media at 25°C in 25 mL culture flasks. Sphaeroforma arctica, Creolimax fragrantissima, and Chromosphaera perkinsii were grown in liquid Marine Broth (Difco™ Marine Broth 2216) at 17°C.

extract_protocol:
Nitrogen liquid grinding followed by NEB Monarch Genomic DNA Purification Kit was used to extract the DNA of all samples. RNA was extracted using the Monarch Total RNA Miniprep Kit.
We used 200 ng of RNA from the samples to build mRNA-seq libraries, first enriching for poly-A transcripts with the NEB Magnetic mRNA Isolation Kit S1550S, and then building the libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L) according to manufacturer's instructions.

treatment_protocol: Amoebidium appalachense DNA and RNA were extracted from cultures grown for 3 days in 10ml 10% BHI with 1% DMSO, and 1% DMSO with 100µM of 5-Azacytidine/Zebularine/Decitabine, in triplicate. Sphaeroforma arctica DNA was extracted from cultures grown for 3 days in 10ml Marine Broth with 1% DMSO and 1% DMSO with 100 µM 5-Azacytidine in duplicate.

value: Axenic culture

tag: growth conditions

value: Brain Heart Infusion (10% BHI, ThermoFisher CM1135) liquid media at 25C

tag: library type

value: mRNA-seq

tag: time

value: 3 days culture


title: Anaerobic stationary phase rep4

description:
invitro_stationary_phase_raw_counts.txt, column S4
htseq count file
invitro_stationary_phase_raw_counts.txt


title: mice cecal content,M rep7

description:
invivo_raw_counts.txt, S7
htseq count file
invivo_raw_counts.txt


title: RNAseq_Aapp_Dev_5h_rep1

description: In the TPM table, column named 5h1

source_name: Reference genome

value: Reference genome

value: 5 hours culture


title: RNAseq_Aapp_Dev_14h_rep2

description: In the TPM table, column named 14h2

value: 14 hours culture


title: RNAseq_Aapp_Dev_14h_rep1

description: In the TPM table, column named 14h1


title: RNAseq_Aapp_Aza_rep2

description: In the TPM table, column named AZA2

value: 1% DMSO and 100uM 5-Azacytidine


title: RNAseq_Aapp_DMSO_rep1

description: In the TPM table, column named DMSO1

value: 1% DMSO


title: Anaerobic stationary phase rep1

description:
invitro_stationary_phase_raw_counts.txt, column S1
htseq count file
invitro_stationary_phase_raw_counts.txt


title: Anaerobic exponential phase rep4

description:
invitro_exponential_phase_raw_counts.txt, S4
htseq count file
invitro_exponential_phase_raw_counts.txt


title: RNAseq_Aapp_Aza_rep1

description: In the TPM table, column named AZA1


title: RNAseq_Aapp_DMSO_rep3

description: In the TPM table, column named DMSO3


title: Anaerobic exponential phase rep3

description:
invitro_exponential_phase_raw_counts.txt, S3
htseq count file
invitro_exponential_phase_raw_counts.txt


title: RNAseq_Aapp_Isolate9256


title: RNAseq_Aapp_Isolate9255


title: EMseq_Aapp_Dev_20h_rep1

data_processing:
Enzymatic Methyl-seq: All reads were filtered and trimmed with fastp using default parameters. Then the trimmed reads mapped to the reference genome (including a lambda phage and pUC19 sequences as negative and positive controls) using BS-Seeker2 backed with bowtie2. Sambamba (markdup) was used to remove PCR duplicates and CGmapTools was used to obtain the methyl calls, resulting in the CGmap files in this repository. More information on this file format here: https://github.com/BSSeeker/BSseeker2.
RNA-seq: All reads were filtered and trimmed with fastp. To obtain TPMs, we used Kallisto (0.46) against the reference mRNA annotation using default parameters. To obtain a counts file we first used HISAT2 allowing multimapping reads, and then used the TElocal pipeline to obtain counts from the bam files. De novo transcriptome assemblies were obtained using Trinity-v2.8.5 using stranded information and the jaccard_clip option.
Assembly: For all the Amoebidium appalachense experiments, the data was mapped to the reference genome that can be found in ENA number ERZ21989579. Sphaerforma assembly is found here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_008580545.1/. Creolimax fragrantissima assembly is found here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002024145.1/. Chromosphaera perkinsii genome can be found here: https://figshare.com/articles/dataset/Genome_-_Chromosphaera_perkinsii/5426494.
Supplementary files format and content: CGmap files are the direct output from CGmapTools / BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain:  (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C /
Supplementary files format and content: Counts / TPM matrixes contain the reads count obtained from the TEcount pipeline (https://github.com/bodegalab/tecount) or the TPMs obtained from Kallisto. Trinity fasta files are the de novo transcriptome assembly for each RNA-seq library.
Library strategy: Enzymatic Methyl-seq

extract_protocol:
Nitrogen liquid grinding followed by NEB Monarch Genomic DNA Purification Kit was used to extract the DNA of all samples. RNA was extracted using the Monarch Total RNA Miniprep Kit.
Enzymatic Methyl-seq samples were performed as per manufacturer's instructions (https://www.neb.com/en-gb/products/e7120-nebnext-enzymatic-methyl-seq-kit) starting from 100 ng of DNA, after sonicating DNA to 300 bp fragments with a Covaris M220.

value: Enzymatic Methyl-seq

value: 20 hours culture


title: EMseq_Aapp_Dev_20h_rep2


title: EMseq_Aapp_Dev_14h_rep2


title: RNAseq_Aapp_Isolate9181


title: EMseq_Aapp_Dev_33h_rep1

value: 33 hours culture


title: RNAseq_Aapp_Dev_20h_rep2

description: In the TPM table, column named 20h2


title: EMseq_Aapp_Decitabine_rep4

value: 1% DMSO and 100uM Decitabine

value: 4 days culture


title: EMseq_Aapp_Dev_5h_rep1


title: EMseq_Aapp_Decitabine_rep3


title: RNAseq_Aapp_Dev_5h_rep2

description: In the TPM table, column named 5h2


title: RNAseq_Aapp_Dev_33h_rep2

description: In the TPM table, column named 33h2


title: RNAseq_Aapp_Dev_20h_rep1

description: In the TPM table, column named 20h1


title: EMseq_Aapp_Zebularine_rep3

value: 1% DMSO and 100uM Zebularine


title: EMseq_Aapp_Aza_rep1


title: EMseq_Aapp_DMSO_rep1


title: RNAseq_Aapp_Aza_rep3

description: In the TPM table, column named AZA3


title: EMseq_Aapp_control


title: RNAseq_Aapp_DMSO_rep2

description: In the TPM table, column named DMSO2


title: EMseq_Aapp_Dev_5h_rep2


title: EMseq_Aapp_Decitabine_rep1


title: RNAseq_Aapp_Dev_33h_rep1

description: In the TPM table, column named 33h1


title: EMseq_Aapp_Decitabine_rep2


title: EMseq_Aapp_Zebularine_rep1


title: EMseq_Aapp_Aza_rep2


title: EMseq_Aapp_Zebularine_rep4


title: EMseq_Aapp_Dev_33h_rep2


title: EMseq_Aapp_Zebularine_rep2


title: Satellite-stem-cells_O_1

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

data_processing:
ATAC-seq data processing and alignment were completed using the Harvard pipeline (https://informatics.fas.harvard.edu/atac-seq-guidelines.html). The GRCm38.p6/mm10 genome primary assembly build used for alignment was obtained from the ensemble database (http://asia/ensembl.org/Musc_musculus/Info/Index;ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa)
All fastq files were trimmed to remove the Illumina Nextera Transposase adapter sequence using Cutadapt v.2.4 with “-m 20” parameter (Martin, 2011). After trimming, FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to check overall sequence quality and evaluate proper adapter trimming. Bowtie2 (Langmead and Salzberg, 2012) was used to align reads to the GRCm38.p6/mm10 mouse reference genome using “-p 8, –very-sensitive” options. Picard tools (http://broadinstitute.githyb.io/picard/) were used to mark and remove duplicates using the MarkDuplicates tool with default options. All subsequent analyses were performed on deduplicated reads. Samtools (Li et al., 2009) was used to sort and obtain uniquely mapped reads using “-b -q 10” options. Samtools were also used to remove reads from the mitochondrial chromosome.
Finally, for visualization purposes, BAM files were converted to an index binary format bigWig using bedtools (Quinlan, 2014).
Peak calling was produced in accordance with Corces et al. 2018 to ensure reproducible high-quality fixed-with peaks with a minimal bias due to change in read depth (ranged from 12,870,021 to 121,543,847 ) and data quality (FROT ranged from 5.1 to 39.7).
Assembly: mm10
Supplementary files format and content: bigWig (.bw), narrowPeak, summits.bed, bed format with score per million score (scpm.bed), bed format and gtf format as well as the counts within the unviersal peak set.

organism: Mus musculus

source_name: Satellite stem cells

extract_protocol:
The tissues of 5 healthy animals were pooled per-replicate for cell isolation, with 3-5 replicates (totalling 15-25 animals) collected per cell type/condition. Multi-omic bulk profiling (OMNI-ATAC-seq assay and RNA-seq) was performed on purified populations collected via fluorescence activated cell sorting (FACS).
OMNI-ATACseq libraries were generated from FACS purified cells according to the standard protocol (Corces et al., 2017). Afterward, libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s recommendations. Library fragments ranging from 150 to 700bp were enriched and the final elution volume was 21ul.

value: Satellite stem cells

value: C57/Bl6 background

value: ~ 22 months


title: Muscle-fibroblasts_Y_1

source_name: Muscle fibroblasts

value: Muscle fibroblasts

value: ~ 2 months


title: Lymph-fibroblasts_Y_2

source_name: Lymph fibroblasts

value: Lymph fibroblasts


title: Lymph-fibroblasts_Y_3


title: Muscle-fibroblasts_O_1


title: EMseq_Aapp_Aza_rep3

value: Reference genome

value: Brain Heart Infusion (10% BHI, ThermoFisher CM1135) liquid media at 25C

value: 3 days culture


title: Lymph-fibroblasts_O_3


title: Lymph-fibroblasts_Y_1


title: EMseq_Aapp_Dev_14h_rep1

value: Axenic culture

value: 14 hours culture


title: EMseq_Aapp_DMSO_rep2

value: 1% DMSO

value: Enzymatic Methyl-seq


title: RNA-Seq Thymic_fibroblasts_Y_3

data_processing:
Demultiplexed single end reads per sample here presented were mapped to the mouse GRCm38.p6/mm10 genome primary assembly using Spliced Transcripts Alignment to a Reference (STAR) software version 2.5.2b (Dobin et al. Bioinformatics 2013; https://doi.org/10.1093/bioinformatics/bts635). STAR was run with mode alignReads with parameters “--outFileterMatchMinOverLred 0.3 --outFilerScoreMinOverLread 0.3 --twopassMode Basic –sjdbGTFfile –quanMode GeneCounts”. Reads with duplicated UMIs were removed using the software Je version 2.0.RC option markdupes (Girardot et al. BMC Bioinformatics, 2016; https://doi.org/10.1186/s12859-016-1284-2). Transcript quantification was performed using featureCounts version 2.0.1 with parameters “–Q10 -M" (exonic regions of GENCODE’s vM24 annotation version) (Liao et al. NAR 2019; https://doi.org/10.1093/nar/gkz114).
Assembly: mm10
Supplementary files format and content: (.txt) counts

source_name: Thymus

growth_protocol: The tissues of 5 healthy animals were pooled per-replicate for cell isolation, with 3-5 replicates (totalling 15-25 animals) collected per cell type/condition. Multi-omic bulk profiling (OMNI-ATAC-seq assay and RNA-seq) was performed on purified populations collected via fluorescence activated cell sorting (FACS).

extract_protocol:
RNA-seq
Poly-A based RNA sequencing libraries were generated as described by us (Sun et al.  Nat Comms 2021;  https://doi.org/10.1038/s41467-021-22863-0.). In brief, a 3-prime biased approach was used to generate sequencing libraries. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template-switching oligonucleotide. The Illumina P5 (5′-AAT GAT ACG GCG ACC ACC GA-3′) and P7 (5′-CAA GCA GAA GAC GGC ATA CGA GAT-3′) sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilises a custom primer (5′-GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C-3′) to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification.
For RNA sequencing, a 3-prime biased approach was used to generate sequencing libraries as described previously (Sun et al.  Nat Comms 2021;  https://doi.org/10.1038/s41467-021-22863-0.). Barcoded 19bp R1 and 111bp R2 paired-end reads per sequencing lane were assigned to individual samples using the sabre software (version 80faf94) with options “-u –m2 –l 10’ (https://github.com/najoshi/sabre) (Tsyganov et al. JOSS 2018; https://doi.org/10.21105/joss.00583).

value: Thymus

value: Thymic fibroblasts

value: 2 months


title: Kidney-tubular_Y_1

source_name: Kidney tubular

value: Kidney tubular


title: Kidney-tubular_O_3


title: Satellite-stem-cells_O_3

value: Satellite stem cells


title: RNA-Seq Thymic_fibroblasts_O_4

value: C57/Bl6 background

value: 22-24 months


title: Fat-progenitors_Y_4

source_name: Fat progenitors

value: Fat progenitors


title: Vessel,T48h Hb Treatment, 02

city: Houston

first: Shafeeque

last: Mohammedali

state: Texas

address: 6431 Fannin St.

institute: UTH Health Houston

data_processing:
Fastq files generated were analyzed manually using the RNA Detector platform HISAT2 alignment has been executed and mapping reads of all files were ≥79%, then differential expression performed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab limited file contain normalised counts for each samples

source_name: cerebral artery

extract_protocol:
Total RNA isolation was performed using RNeasy® Mini Kit (Qiagen CatNo:74104), for which the initial sample mincing was carried out on dry ice with sterilized, pre-chilled blade and pipette tips to avoid degradation of RNA, then transferred to RLT lysis buffer containing beta-mercaptoethanol. Other than this initial set of sample processing, the rest of the steps, including DNase I treatment, were followed as instructed in the protocol.
Total RNA was quality-checked using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). RNA with an integrity number of greater than 7 was used for library preparation. Libraries were prepared with SMART-Seq V4 PLUS Kit (R400752, Takara Bio, Japan) following the manufacturer’s instructions. The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) , library concentrations were determined by qPCR using Collibri Library Quantification kit (#A38524500, Thermo Fisher Scientific). The libraries were pooled evenly and went for the paired-end 75-cycle sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).

treatment_protocol: HB vessels for 48 hours treatment was employed with Human Hb (64,500 Da; Sigma-Aldrich, St. Louis, Missouri, USA) in culture. We have prepared stock in 1X PBS and diluted to 25uM by using culture media, media changed once after 24 hours.

value: cerebral artery

value: Hemoglobin


title: RNA-Seq Thymic_fibroblasts_Y_4


title: Vessel,T48h Hb Treatment, 01


title: RNA-Seq Thymic_fibroblasts_Y_1


title: RNA-Seq Thymic_epithelial_Y_5

value: Thymic epithelial


title: Vessel,T0 control, 03


title: Lymph-fibroblasts_O_4

value: Lymph fibroblasts

value: ~ 22 months


title: RNA-Seq Thymic_epithelial_Y_4


title: Muscle-fibroblasts_O_3

value: Muscle fibroblasts


title: EMseq_Aapp_DMSO_rep3

value: Reference genome

value: Brain Heart Infusion (10% BHI, ThermoFisher CM1135) liquid media at 25C

value: 3 days culture


title: Vessel,T0 control, 01


title: Lymph-fibroblasts_Y_4

value: ~ 2 months


title: Vessel,T48h Hb Treatment, 03


title: RNA-Seq Thymic_fibroblasts_O_3

value: Thymus

value: Thymic fibroblasts


title: RNA-Seq Thymic_fibroblasts_Y_2

value: 2 months


title: Satellite-stem-cells_O_2

value: Satellite stem cells


title: 23971hcp MOUSE 10

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Standard Illumina base-calling pipelines using bcl2fastq v2.20 were used to make fastqs.
Fastqs were processed using TrimGalore v0.6.6 in paired-end mode using default parameters.
Validated read pairs were then aligned to the GRCm38.v5 mouse genome using Hisat2 v2.1.0 with parameters --dta --no-softclip --no-mixed --no-discordant. The resulting hits were filtered to remove mappings with a MAPQ scores of < 20 and then converted to BAM format using Samtools v1.10.
Allele-specific alignments were also performed by realigning mapped reads to N-masked genomes C57Bl/6 (genome 1) and CAST_EiJ (genome 2) which was based on the GRCm38.v5 genome, and generated using the SNPsplit package (v0.3.4; https://github.com/FelixKrueger/SNPsplit). Reads that were then sorted by allele-specifically for either genome and reads containing conflicting SNP information were excluded.
Total and allele specific read counts were quantified from BAMs with featureCounts (from the subread package v2.0.0) using default parameters with gencode vM25 annotations. Total counts were further normalised to transcripts per million (TPM) using a custom R-script.
Assembly: GRCm38.v5
Supplementary files format and content: hippocampus_rnaseq_featureCounts_all_counts_27092022.txt contains the total read counts from featureCounts for each sample where columns are individual samples and rows are genes.
Supplementary files format and content: hippocampus_rnaseq_featureCounts_TPM_27092022.txt contains normalised read counts as transcripts per million (TPM) for each sample where columns are individual samples and rows are genes.
Supplementary files format and content: hippocampus_rnaseq_featureCounts_allelic_counts_27092022.txt contains the alele specific read counts from featureCounts for each sample where columns are individual alleles of each sample and rows are genes.

growth_protocol: Reciprocal crosses between BL6 and CAST animals - BL6/CAST (BL6 female and CAST male) and CAST/BL6 (CAST female and BL6 male) were established to generate F1 animals. Mice were maintained under normal conditions:five per cage in a temperature- and humidity-controlled room (24°C, 45-65%) with a 14/12hr light/dark cycle.

extract_protocol:
Total RNA was extracted from cells using Nucleo Spin TriPrep kit (Macherey-Nagel GmbH & Co.KG, Germany) according to manufacturer’s instructions.
RNA was used as input for PolyA+ directional RNA-seq library preparation using the NEBNext Ultra II Directional RNA-seq Kit (#E7765, NEB) with the PolyA mRNA magnetic isolation module (#E7490, NEB) according to the manufacturers instructions. The pooled library was sequenced on an Illumina HiSeq 2000 with a 2x100 kit.

treatment_protocol: Juvenile and old F1 animals were developed and sacrificed respectively in the range of 8-9 weeks and 102-104 weeks. Culled mice had their hippocampus extracted  according to the atlas of stereotaxic coordinates of mouse brain (Paxinos and Franklin, 1997) and homogenised.

tag: age category

value: young

tag: Sex

value: female

tag: mother strain

value: Cast

tag: father strain

value: BL&

tag: strain cross

value: Cast x BL6

tag: age weeks

tag: library format

value: 100bp PE


title: RNA-Seq Thymic_epithelial_O_4

tag: cell type

value: Thymic epithelial

value: C57/Bl6 background

value: 22-24 months


title: Vessel,T0 control, 02

tag: tissue

value: cerebral artery


title: Vessel,T48h control, 02


title: RNA-Seq Thymic_fibroblasts_O_2

tag: genotype


title: 1622hcp MOUSE 6


title: RNA-Seq Thymic_epithelial_O_3

tag: treatment


title: RNA-Seq Thymic_fibroblasts_O_1


title: RNA-Seq Thymic_epithelial_Y_3


title: RNA-Seq Thymic_epithelial_O_2


title: Subject 41 pre treatment

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA)
Fastq files were trimmed for adapters.
Trimmed reads were mapped to the reference human genome hg38 using STAR aligner.
The filtered alignments were quantified to hg38 Ensembl Transcripts release 99
Differential expression was performed using Deseq2
Assembly: Hg38
Supplementary files format and content: .txt

source_name: Breast Biopsy

extract_protocol:
RNA extraction was performed from 16 paired samples using the PurelinkTM RNA Micro kit in conjunction with TRIzol reagent (Life Technologies) as per the standard manufacturer’s protocol.
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014)

value: Breast Biopsy


title: Vessel,T48h control, 01


title: RNA-Seq Thymic_epithelial_Y_2


title: RNA-Seq Thymic_epithelial_Y_1


title: Subject 56 post treatment

value: 50 mg mifepristone


title: Subject 56 pre treatment


title: 1681hcp MOUSE 9

value: BL6 x Cast


title: 999hcp MOUSE 1

value: old


title: Subject 38 post treatment


title: Subject 49 post treatment


title: 1679hcp MOUSE 8


title: 1678hcp MOUSE 7


title: Subject 49 pre treatment


title: RNA-Seq Thymic_epithelial_O_5

value: Thymus


title: Kidney-tubular_O_1

value: Kidney tubular

value: ~ 22 months


title: Subject 41 post treatment


title: Subject 38 pre treatment


title: 734hcp MOUSE 11


title: RNA-Seq Skin_fibroblasts_Y_2

source_name: Skin

value: Skin

value: Skin fibroblasts

value: 2 months


title: mgROOT2

city: Winnipeg

first: Mark

last: Belmonte

state: Manitoba

address: 50 Sifton Rd.

department: Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
low quality reads were trimmed and aligned to the B. napus cv. Topas reference genome using hisat2. Quantification of uniquely mapped reads were done using the featurecounts package. Counts were normalized to TPM.
Assembly: Brassica napus cv. Topas
Supplementary files format and content: Tab delimited text file of normalized TPM values. Raw data uploaded to SRA.

organism: Brassica napus

source_name: Brassica napus embryo proper

growth_protocol: B. napus plants were grown in growth chambers nder long day cycles (16 h light, 8 h dark, 22°C, RH 50%–70%)

extract_protocol:
Once dissection was completed, total RNA was extracted using Ambion RNaqueous micro kit with Qiagen RNAse-free Dnase to remove genomic DNA. RNA quality was evaluated using an Agilent Bioanalyzer. Minimum RIN of 3 was required for further processing.
Fragmentation was conducted via Covaris ultra-sonicator. Library preparation was done with NuGen Ovation Multiplex System. Libraries were quantified and assessed in quality via Quant-iT PicoGreen dsDNA assay kit, qPCR, and the High Sensitivity DNA analysis kit (Agilent) on the Agilent 2100 Bioanalyzer. Libraries were pooled and size selected at 350-600 bp on an E-Gel (Invitrogen). Samples were sequenced on the Illumina HiSeq 2000 platform.

treatment_protocol: Flowers were hand pollinated at the time of anthesis during the times of 14:00 - 17:00. Siliques were collected at 0 (ovule), 7 (globular), 10 (heart), and 28 (mature green) days after pollination. Tissue was fixed in 1:3 (v/v) glacial acetic acid: 85% ethanol for 24 h at 4°C. Tissue was dehydrated in a graded ethanol series, then infiltrated with molten parrafin wax at 60°C. Tissue was then embedded in 100% paraffin wax and 7 µm sections were cut onto polyethylene napthalate membrane slides for LMD. Sections were deparaffinized and subregions were dissected and isolated out using LMD.

tag: cultivar

value: Topas

value: Brassica napus embryo proper

value: Brassica napus cv. Topas


title: Subject 31 post treatment


title: 1086hcp MOUSE 4

value: female

value: Cast

value: Cast x BL6

value: 100bp PE


title: RNA-Seq Skin_fibroblasts_Y_1

value: C57/Bl6 background


title: 1084hcp MOUSE 3


title: RNA-Seq Thymic_epithelial_O_1

value: Thymic epithelial

value: 22-24 months


title: RNA-Seq Skin_fibroblasts_O_3


title: 1000hcp MOUSE 2

value: old

value: BL6 x Cast


title: RNA-Seq Skin_fibroblasts_Y_3


title: mgOSC1

source_name: Brassica napus seed coat

value: Brassica napus seed coat


title: 1619hcp MOUSE 5

value: young


title: mgISC1


title: mgCZSC3


title: Subject 24 pre treatment

value: Breast Biopsy


title: mgROOT1


title: RNA-Seq Skin_fibroblasts_O_1

value: Skin

value: Skin fibroblasts


title: mgCOT2

value: Topas


title: mgCOT3

value: Brassica napus embryo proper


title: Subject 23 pre treatment


title: mgCOT1

value: Brassica napus cv. Topas


title: mgCPT1

source_name: Brassica napus endosperm

value: Brassica napus endosperm


title: Subject 31 pre treatment


title: RNA-Seq Satellite_stem_cells_O_3

source_name: Muscle

value: Muscle

value: Satellite stem cells


title: Subject 24 post treatment

value: 50 mg mifepristone


title: mgISC2


title: hPEN1


title: RNA-Seq Skin_fibroblasts_O_2

value: C57/Bl6 background


title: mgCZSC2


title: Subject 16 post treatment


title: RNA-Seq Satellite_stem_cells_Y_3

value: 2 months


title: mgCZSC1

source_name: Brassica napus seed chalaza

value: Brassica napus seed chalaza


title: Subject 23 post treatment


title: hMCE3


title: hMCE4


title: mgCPT2


title: mgCPT3


title: hMCE1


title: hMCE2


title: mgOSC2


title: RNA-Seq Satellite_stem_cells_O_1

value: 22-24 months


title: Subject 20 post treatment


title: Subject 15 post treatment


title: hEP3


title: hCZE2


title: RNA-Seq Neurons_Y_4

source_name: Cerebrum

value: Cerebrum

value: Neurons


title: RNA-Seq Satellite_stem_cells_Y_1


title: hCZE1


title: Subject 20 pre treatment


title: hPEN2


title: RNA-Seq Satellite_stem_cells_Y_2


title: RNA-Seq Satellite_stem_cells_O_2


title: hEP2


title: Subject 15 pre treatment


title: hEP1


title: Subject 16 pre treatment


title: RNA-Seq Neurons_Y_3


title: hISC3

value: Brassica napus seed coat


title: RNA-Seq Neurons_O_2


title: hISC1


title: hISC2


title: hCZSC3


title: RNA-Seq Muscle_fibroblasts_Y_2

value: Muscle fibroblasts


title: Subject 7 post treatment

value: Breast Biopsy


title: hOSC3


title: hOSC2


title: hCPT2


title: Subject 14 pre treatment


title: RNA-Seq Neurons_O_4


title: Subject 8 post treatment


title: hCPT3


title: hCPT1


title: gCZE3


title: gCZE1


title: Subject 14 post treatment


title: Subject 8 pre treatment


title: RNA-Seq Neurons_O_1


title: hCZSC2


title: RNA-Seq Muscle_fibroblasts_Y_3


title: RNA-Seq Muscle_fibroblasts_O_2


title: hCZSC1


title: Subject 7 pre treatment


title: RNA-Seq Muscle_fibroblasts_Y_1


title: gMCE4


title: gCZE2


title: Subject 2 post treatment


title: Subject 2 pre treatment


title: Subject 4 post treatment


title: Subject 4 pre treatment


title: hOSC1


title: RNA-Seq Muscle_fibroblasts_O_3


title: RNA-Seq Muscle_fibroblasts_O_1


title: gPEN1


title: gPEN2


title: RNA-Seq Lymph_fibroblasts_Y_1

source_name: Lymph nodes

value: Lymph nodes

value: Lymph fibroblasts


title: gMCE5

value: Topas


title: ST2_Arid5a_4_IL17

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5051 Centre Avenue, 4051

department: Microbiology and Immunology

institute: University of Pittsburgh

description: after treatment, formaldhyde crosslinking followed by Arid5a RIP

data_processing:
The raw sequence reads were mapped to mm10 using default parameters in STAR (v2.7.9) and quantified using RSEM (v1.3.1)
Read count extraction and normalization were performed using DESeq2 (v1.36.0) in R(v4.3.0)
Assembly: mm10
Supplementary files format and content: comma-separated values file include FPKM and count values for each Sample

source_name: mouse stromal cell

growth_protocol: ST2 were plated in 150mm tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator overnight.

extract_protocol:
Cells were trypsinized and crosslinked by 1% formaldehyde (Thermo Scientific). Extracts were isolated with cell lysis buffer II (Invitrogen) with RNase Inhibitor (40 U/μl; Thermo Scientific). Buffers included protease inhibitor cocktail (Sigma-Aldrich). Lysates were immunoprecipitated with Abs against Arid5a or mouse IgG2b. Beads were washed with lysis buffer and digested with DNase I (Roche Applied Science) and protease K (Sigma-Aldrich). Total RNA was extracted with acid phenol.
SMART-Seq Stranded kit from Takara

treatment_protocol: Cells were stimulated with IL-17 (200 ng/mL) or medium control for 3 hours .

value: mouse stromal cell

tag: cell line

value: mouse stromal cell line

tag: rip antibody

value: Arid5a; Cat# MA5-18292; Invitrogen Lot YH4037297B


title: RNA-Seq Lymph_fibroblasts_O_3


title: gMCE3

value: Brassica napus endosperm

value: Brassica napus cv. Topas


title: RNA-Seq Lymph_fibroblasts_Y_3

value: C57/Bl6 background


title: gMCE2


title: ST2_Arid5a_3_IL17


title: gOSC2


title: gOSC1


title: gMCE1


title: gISC3


title: gEP4

value: Brassica napus embryo proper


title: RNA-Seq Lymph_fibroblasts_Y_2

value: 2 months


title: gEP2


title: Subject 1 pre treatment


title: gEP3


title: gEP1


title: RNA-Seq Lymph_fibroblasts_O_2

value: 22-24 months


title: RNA-Seq Lymph_endothelial_Y_3

value: Lymph endothelial


title: gCZSC1


title: ST2_Arid5a_2_IL17


title: gCPT3

value: Brassica napus seed chalaza


title: gISC2

value: Brassica napus seed coat


title: gISC1


title: ST2_IgG_3_IL17

description: after treatment, formaldhyde crosslinking followed by IgG2b RIP

value: Mouse IgG2b; Cat# 53484S; CST Lot 1


title: RNA-Seq Lymph_fibroblasts_O_1


title: ovOSC3


title: ST2_IgG_2_IL17


title: gCPT1


title: ovOSC2


title: RNA-Seq Lymph_endothelial_Y_4


title: ST2_Arid5a_4_Med

value: medium control


title: ovOSC1


title: Subject 1 post treatment

value: Breast Biopsy

value: 50 mg mifepristone


title: gCZSC3

value: Topas


title: ovISC2


title: gCZSC2


title: ST2_Arid5a_3_Med

value: mouse stromal cell


title: ovISC3


title: ST2_IgG_4_IL17

value: mouse stromal cell line


title: RNA-Seq Lymph_endothelial_Y_2

value: Lymph nodes


title: gCPT2


title: RNA-Seq Lymph_endothelial_O_1


title: ovISC1


title: ST2_Arid5a_2_Med

value: Arid5a; Cat# MA5-18292; Invitrogen Lot YH4037297B


title: ST2_Arid5a_1_IL17


title: ovCZSC3

value: Brassica napus cv. Topas


title: RNA-Seq Lymph_endothelial_O_3

value: C57/Bl6 background


title: RNA-Seq Liver_progenitors_Y_3

source_name: Liver

value: Liver

value: Liver Progenitors


title: ST2_Arid5a_1_Med


title: ovCZSC1


title: RNA-Seq Lymph_endothelial_O_2

value: 22-24 months


title: RNA-Seq Liver_progenitors_Y_2

value: 2 months


title: ovCPT2

value: Brassica napus seed chalaza


title: ST2_IgG_4_Med


title: ovCZSC2


title: ST2_IgG_2_Med


title: MOLM-13_Ctrl_MLL-AF9_rep2

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Reads were aligned using bowtie2 v2.3.4.1.
For CUT&Tag, normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Assembly: hg38, mm10
Supplementary files format and content: BigWig files contains normalized read count (CPM, in 50-bp bins)
Library strategy: CUT&Tag

growth_protocol: Human cells HEL and MOLM-13 were cultured in 90% RPMI-1640 + 10% FBS + 2% Penicillin/Streptomycin.

extract_protocol:
DNA was extracted by Phenol-Chloroform-Isoamylol and amplified by PCR
Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation.  DNA was extracted and amplified by PCR. The product was purified by AMpure XP beads. After size seletion of purified production, library will be analyzed by Illumina NovaSeq 6000.

value: acute myeloid leukemia

tag: cut&tag antibody

value: AF9 (diagenode, C15310266)


title: RNA-Seq Liver_progenitors_O_2


title: ovCPT1


title: RNA-Seq Liver_progenitors_O_1


title: RNA-Seq Kidney_tubular_Y_3

source_name: Kidney

value: Kidney

value: Kidney tubular


title: MOLM-13_AF9KO_MLL1_rep1

value: MLL1 (456, thanks to E. Canaani lab)


title: MOLM-13_AF9KO_MLL-AF9_rep2


title: A5_Ezh2I_2_S28

description:
ATAC_Fosl2_Ezh2i_peaks.gtf
ATAC_Fosl2_Ezh2i.counts.txt

data_processing:
ATAC-seq: Peak calling was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01”. Then, peak summits were extended by 250 bp on both sides  to a final width of 501 bp. Peaks were filtered for mm10 blacklisted regions   (https://www.encodeproject.org/annotations/ENCSR636HFF/).
As in Corces et al. 2020 per sample overlapping peaks were handled using an iterative removal approach. That is in case of two overlapping peaks the most significant peak is kept and the other removed. This process is performed in an iterative manner, so all peaks have been kept or removed based on their overlap and significance score. This method results in a set of fixed-width peaks per sample.
Next, significance peak scores “(-log10(p-value))” were converted to a score per million value by dividing each individual peak score by the sum of all of the peak scores in the given sample divided by 1 million.  This normalized score per million value corrects the original peak calling scores for sample sequencing depth and quality, as higher quality samples yield higher number of peaks and higher significance scores overall. Thus, scores per million allow the direct comparison of peaks across biological replicates.
Next, we compiled a condition - MEF, mESC- and sequencer specific - BGI, Illumina - peak set containing reproducible peaks observed in a particular cell type and sequencing platform. For that, we generated a cumulative peak set per cell type and sequencing platform and performed the same iterative approach as mentioned above. Therefore, maintaining the peak with the highest significance or score per million. Only peaks with a score per million value >=3 observed in at least two samples (minimal overlap 50%) were further considered.
Assembly: mm10
Supplementary files format and content: Matrix table with counts per peaks in (.txt) format, samples mapping in bigwig format (.bw) and peaks called per individual sample as (.txt) format.
Library strategy: Omni ATAC-seq

source_name: mouse embryonic fibroblasts

extract_protocol: We transduced mouse embryonic fibroblasts with a CRISPRa-VPR–mCherry construct and assessed more immediate and longer term effects of Fra2 over-expression by performing OMNI-ATACseq on FACS purifed mCherry+/THY1+ cells 4 and 11 days following lentiviral infection with Fra2 gRNAs or scrambled control.For Ezh2 inbition:Following three days of treatment with the Ezh2 inhibitor (Sigma-Aldrich, GSK343) at 4μM and a washout day, MEFs were submitted to the ATAC-seq assay.

value: mouse embryonic fibroblasts

value: C57/B16 background

value: Day 4


title: ST2_IgG_3_Med

value: mouse stromal cell

value: mouse stromal cell line

value: Mouse IgG2b; Cat# 53484S; CST Lot 1

value: medium control


title: HEL_AF9shRNA2_AF9KD_TBP_rep2

source_name: HEL

value: HEL

value: Human erythroblast

value: TBP (Santa, SC-56795)


title: RNA-Seq Liver_progenitors_O_3

value: Liver

value: Liver Progenitors

value: C57/Bl6 background

value: 22-24 months


title: MOLM-13_Ctrl_MLL1_rep2

value: acute myeloid leukemia


title: MOLM-13_AF9KO_MLL1_rep2


title: RNA-Seq Liver_progenitors_Y_1

value: 2 months


title: A4_Ezh2I_1_S27


title: MOLM-13_Ctrl_MLL-AF9_rep1

value: AF9 (diagenode, C15310266)


title: ST2_IgG_1_Med


title: A3_ENeg_3_S3

value: mouse embryonic fibroblasts

value: scrambled control


title: A6_Ezh2I_3_S29

value: C57/B16 background

value: Day 4


title: TC A2 IgG

data_processing:
*library strategy: CUT&RUN
Fastq files were trimmed and aligned using CUT&RUNTools2183 (v 2.0), with de-duplicated BAM files retaining <120bp fragments used for further analysis.
The NEBNext adaptor sequences AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (paired end 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (paired end 2) were supplied for trimming.
In order to plot aggregate signals for the factors, we first generated bigWig files of normalised (CPM) coverage either of individual or merged (after merging the replicates with samtools149 merge) samples using the Deeptools155 bamCoverage program with paramaters ----normalizeUsing CPM and --binSize 10 for the factors Ctcf, p63, Gata3 and Tcf1 and --binSize 50 and --smoothLength 100 for Jun. BigWig files for matched IgGs were also generated with matched parameters in bamCoverage.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Spleen

extract_protocol:
The tissues of 5 healthy animals were pooled per-replicate for cell isolation, with 3-5 replicates (totalling 15-25 animals) collected per cell type/condition. Cell-types were purified populations collected via fluorescence activated cell sorting (FACS).
The CUT&RUN protocol was adapted from the EpiCypher® CUTANA™ CUT&RUN Protocol v1.7, with the parameters suggested for TF detection. As a modification, DNA fragments were purified via Spin Columns (Cell Signalling, CST14209) according to the manufacturer’s instructions.

value: Spleen

value: CD8 Naive T-cells

tag: strain background

value: 22 months


title: MOLM-13_Ctrl_MLL1_rep1

value: MLL1 (456, thanks to E. Canaani lab)


title: MOLM-13_AF9KO_MLL-AF9_rep1


title: RNA-Seq Kidney_tubular_Y_2

value: Kidney

value: Kidney tubular


title: HEL_AF9shRNA2_AF9KD_TBP_rep1

value: HEL

value: Human erythroblast

value: TBP (Santa, SC-56795)


title: Vessel,T48h control, 03

value: cerebral artery


title: HEL_AF9shRNA2_Ctrl_AF9_rep2


title: RNA-Seq Kidney_tubular_Y_1

value: C57/Bl6 background


title: TC A1 IgG

tag: time


title: RNA-Seq Kidney_tubular_O_2

value: 22-24 months


title: HEL_AF9shRNA2_Ctrl_TBP_rep1


title: RNA-Seq Kidney_tubular_O_4


title: HEL_MLL1shRNA2_Ctrl_AF9_rep2


title: HEL_AF9shRNA2_Ctrl_MLL1_rep2

value: MLL1 (468, thanks to E. Canaani lab)


title: TC Y2 IgG

value: 8 weeks


title: HEL_AF9shRNA2_AF9KD_AF9_rep2


title: RNA-Seq Kidney_endothelial_Y_4

value: Kidney endothelial

value: 2 months


title: HEL_AF9shRNA2_Ctrl_TBP_rep2


title: CUT&RUN-HUSH, WT, TASOR

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

data_processing:
Reads were aligned using bowtie2 and quantification was performed using deepTools.
Assembly: hg38
Supplementary files format and content: bigwig files normalised as RPKM
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed on 500,000 K562 cells using the CUTANA CUT&RUN kit (EpiCypher) following the manufacturer's instructions.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina

value: WT

tag: antibody

value: TASOR


title: CUT&RUN-IRF2, TAS2KO, TASOR2

value: TASOR2 KO


title: RNA-Seq Kidney_endothelial_Y_3


title: CUT&RUN-IRF2, IRF2KO, TASOR2

value: IRF2 KO


title: RNA-Seq Kidney_endothelial_Y_2


title: HEL_AF9shRNA2_AF9KD_MLL1_rep2


title: TC A2 Tcf1

value: Spleen

value: CD8 Naive T-cells

value: 22 months


title: RNA-Seq Kidney_tubular_O_3

value: Kidney

value: Kidney tubular


title: HEL_MLL1shRNA2_MLL1KD_AF9_rep2

value: HEL

value: Human erythroblast


title: CRISPRi-IRF2, sg1-IRF2, rep2

data_processing:
Reads were trimmed with cutadapt and aligned using bowtie2. Further analysis was performed in SeqMonk using the RNA-seq pipeline.
Assembly: hg38
Supplementary files format and content: Tab-delimited file showing normalised and log2-transformed RPKM values for each sample

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (QIAGEN) and treated with DNaseI (QIAGEN). Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit v2 (NEB).
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer's instructions.


title: TC A1 Tcf1


title: HEL_MLL1shRNA2_MLL1KD_MLL1_rep2


title: RNA-Seq Kidney_tubular_O_1

value: C57/Bl6 background


title: HEL_MLL1shRNA2_Ctrl_MLL1_rep2


title: CRISPRi-IRF2, sgAAVS1, rep1


title: TC Y1 IgG


title: CUT&RUN-HUSH, TASORKO, TASOR

value: TASOR KO


title: TC Y1 Tcf1


title: RNA-Seq Kidney_endothelial_O_2

value: 22-24 months


title: TC A2 Jun


title: CRISPRi-IRF2, dCas9, rep1

value: untransduced


title: TC Y2 Jun

value: 8 weeks


title: KC A4 Ctcf

value: Skin

value: Keratinocyes


title: CRISPRi-IRF2, sg2-IRF2, rep2


title: CUT&RUN-IRF2, WT, TASOR2

value: WT


title: CRISPRi-IRF2, sg2-IRF2, rep1


title: RNA-Seq Kidney_endothelial_Y_1

value: Kidney endothelial

value: 2 months


title: CRISPRi-HUSH2, sg1-MPP8

data_processing:
Reads were trimmed with cutadapt and aligned using bowtie2. Further analysis was performed in SeqMonk using the RNA-seq pipeline.
Assembly: hg38
Supplementary files format and content: Tab-delimited file showing normalised nad log2-transformed RPKM values for each sample


title: CRISPRi-HUSH2, sg2-MPP8


title: CRISPRi-IRF2, sgAAVS1, rep2


title: CRISPRi-IRF2, sg1-IRF2, rep1


title: RNA-Seq Kidney_endothelial_O_3


title: TC Y2 Tcf1

value: Spleen


title: CRISPRi-HUSH2, sg2-TASOR2


title: KC A4 IgG


title: CRISPRi-IRF2, dCas9, rep2


title: RNA-Seq Keratinocytes_O_3

value: Kerationcytes


title: CRISPRi-HUSH2, sg1-PPHLN1


title: CRISPRi-HUSH2, sg2-PPHLN1


title: CRISPRi-HUSH2, sg3-TASOR2


title: CRISPRi-HUSH2, sgAAVS1, rep1


title: CRISPRi-HUSH2, dCas9, rep2


title: CUT&RUN-L1Vpx, +L1, TASOR2

data_processing:
Reads were aligned using bowtie2 and quantification was performed using deepTools.
Assembly: hg38
Supplementary files format and content: bigwig files normalised as RPKM


title: RNA-Seq Keratinocytes_Y_4


title: KC Y1 IgG


title: RNA-Seq HSC_Y_4

source_name: Bone Marrow

value: Bone Marrow

value: Hematopoietic stem cells


title: RNA-Seq Keratinocytes_Y_3


title: CUT&RUN-L1Vpx, +Vpx, TASOR2

value: +Vpx


title: RNA-Seq Keratinocytes_Y_2


title: CRISPRi-HUSH2, sg1-TASOR2


title: CRISPRi-HUSH2, sgAAVS1, rep3


title: RNA-Seq Kidney_endothelial_O_1

value: Kidney


title: KC A2 IgG

value: 22 months


title: CUT&RUN-L1Vpx, WT, TASOR2


title: RNA-Seq HSC_Y_3

value: C57/Bl6 background


title: CRISPRi-HUSH2, sg2-TASOR


title: RNA-Seq Keratinocytes_Y_1


title: CRISPRi-HUSH2, sg1-TASOR


title: CUT&RUN-HUSH2, TASOR2KO, PPHLN1

value: TASOR2 KO


title: RNA-Seq HSC_Y_2


title: CUT&RUN-L1Vpx, TASOR2KO, TASOR2


title: KC Y4 Ctcf


title: RNA-Seq HSC_Y_1


title: KC Y4 IgG


title: KC Y1 p63


title: CUT&RUN-HUSH2, WT, MPP8


title: CUT&RUN-HUSH2, WT, PPHLN1


title: CRISPRi-HUSH2, dCas9, rep1


title: KC A4 Gata3


title: KC Y2 IgG


title: RNA-Seq Keratinocytes_O_1

value: 22-24 months


title: CRISPRi-HUSH2, sgAAVS1, rep2


title: CUT&RUN-HUSH2, WT, TASOR2


title: KC A4 p63


title: RNA-Seq HSC_O_7


title: CUT&RUN-HUSH, TASORKO, PPHLN1

value: TASOR KO


title: KC Y4 Gata3

value: 8 weeks


title: RNA-Seq Keratinocytes_O_2

value: Skin


title: CUT&RUN-HUSH2, TASOR2KO, IgG

value: IgG


title: KC A1 p63

value: Keratinocyes


title: CUT&RUN-HUSH2, TASOR2KO, MPP8


title: KC Y1 Gata3


title: RNA-Seq HSC_O_5


title: CUT&RUN-HUSH, WT, MPP8

value: WT


title: KC A2 Jun


title: KC Y4 p63


title: CUT&RUN-HUSH2, TASOR2KO, TASOR2


title: PBMCs, HF, 5

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisallee 30

department: Klinik und Poliklinik für Kardiologie

country: Germany

institute: Universitätsklinikum Leipzig

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files generated by bcl2fastq (version 2.20.0.422) were processed with cellranger count (version 6.1.1) against the human hg38 reference including lncipedia_5_2 transcripts.
Assembly: Reference transcriptome consisting of: human hg38 and lncipedia 5.2
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HF patient

growth_protocol: PBMC collection: Control and patient blood was collected in EDTA monovettes and processed immediately. Specifically, blood was diluted in PBS (ThermoFisher, #10010023) and layered onto Histopaque®-1077 (Sigma-Aldrich, #10771). Tubes were centrifuged for 30 min at room temperature, 800 g, brake and speed-up 1, and PBMCs were collected from the interphase between Histopaque®-1077 and plasma. PBMCs were washed five times with PBS, counted and frozen at -80°C in a 1:1 mixture of resuspension (40% FBS in RPMI) and 2x freezing medium (30% DMSO in RPMI containing 40% FBS) according to 10x Genomics demonstrated protocol #CG00039. The next day, PBMCs were transferred to liquid nitrogen for long-term storage.

extract_protocol:
Single cell preparation and barcoding: PBMCs were thawed according to 10x Genomics demonstrated protocol #CG00039 and a cell concentration of 700 to 1,200 PBMCs per µl of PBS + 0.04% BSA was set. Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #PN-1000128, Chip G: #1000127) was used to generate GEMs, reverse transcribe RNA and amplify cDNA according to manufacturer’s instructions. Targeted cell recovery was 10,000.
Library construction and sequencing: After cleanup (step 2.3), 2 µl of the cDNA was used for quality control on the Agilent fragment analyzer (DNF-473 Standard Sensitivity NGS Fragment Kit). In addition, 10 µl of the cDNA was used as input for step 3 of the Chromium Next GEM Single Cell 3´ Reagent Kit to perform fragmentation, end-repair, A-tailing and adapter-ligation. The finished library was monitored again using the fragment analyzer and the DNF-473 Standard Sensitivity NGS Fragment Kit. Equimolar amounts of each sample were plexed at 1.25 nmol/l. Sequencing was performed as paired-end 2x150bp (S4-Flowcell) on a Novaseq 6000 (Illumina).

value: HF patient

value: human PBMCs


title: KC Y2 Jun


title: CUT&RUN-HUSH, PPHLN1KO, PPHLN1

value: PPHLN1 KO


title: RNA-Seq HSC_O_8

value: Bone Marrow


title: KC A1 IgG


title: RNA-Seq HSC_O_3

value: Hematopoietic stem cells


title: RNA-Seq Fat_progenitors_Y_4

source_name: Visceral Fat

value: Visceral Fat

value: Fat progenitors

value: 2 months


title: KC A1 Gata3

source_name: Skin

value: 22 months


title: KC Y1 Jun


title: PBMCs, HF, 1

description: 10x Genomics


title: CUT&RUN-HUSH, MPP8KO, MPP8

value: MPP8 KO


title: CUT&RUN-HUSH, WT, PPHLN1


title: A9_EFosL2_3_S6

data_processing:
ATAC-seq: Peak calling was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01” [34], [35]. Then, peak summits were extended by 250 bp on both sides  to a final width of 501 bp. Peaks were filtered for mm10 blacklisted regions [36]  (https://www.encodeproject.org/annotations/ENCSR636HFF/).
As in Corces et al. 2020 per sample overlapping peaks were handled using an iterative removal approach. That is in case of two overlapping peaks the most significant peak is kept and the other removed. This process is performed in an iterative manner, so all peaks have been kept or removed based on their overlap and significance score. This method results in a set of fixed-width peaks per sample.
Next, significance peak scores “(-log10(p-value))” were converted to a score per million value by dividing each individual peak score by the sum of all of the peak scores in the given sample divided by 1 million.  This normalized score per million value corrects the original peak calling scores for sample sequencing depth and quality, as higher quality samples yield higher number of peaks and higher significance scores overall. Thus, scores per million allow the direct comparison of peaks across biological replicates.
Next, we compiled a condition - MEF, mESC- and sequencer specific - BGI, Illumina - peak set containing reproducible peaks observed in a particular cell type and sequencing platform. For that, we generated a cumulative peak set per cell type and sequencing platform and performed the same iterative approach as mentioned above. Therefore, maintaining the peak with the highest significance or score per million. Only peaks with a score per million value >=3 observed in at least two samples (minimal overlap 50%) were further considered.
Assembly: mm10
Supplementary files format and content: Matrix table with counts per peaks in (.txt) format, samples mapping in bigwig format (.bw) and peaks called per individual sample as (.txt) format.

source_name: mouse embryonic fibroblasts, Fra2 overexpression, day 3

extract_protocol: Omni ATAC-seq

treatment_protocol: We transduced mouse embryonic fibroblasts with a CRISPRa-VPR–mCherry construct and assessed more immediate and longer term effects of Fra2 over-expression by performing OMNI-ATACseq on FACS purifed mCherry+/THY1+ cells 3 and 10 days following lentiviral infection with Fra2 gRNAs or scrambled control

value: mouse embryonic fibroblasts

value: C57/B16 background

value: Day 3


title: PBMCs, Control, 2

description: 10x Genomics

source_name: Control

value: Control


title: RNA-Seq HSC_O_6

value: C57/Bl6 background

value: 22-24 months


title: CUT&RUN-HUSH2, WT, IgG

value: WT

value: IgG


title: PBMCs, Control, 1

description: 10x Genomics

value: human PBMCs


title: RNA-Seq HSC_O_9


title: PBMCs, HF, 7

description: 10x Genomics

value: HF patient


title: A8_EFosL2_2_S5


title: KC A1 Jun

value: Skin

value: Keratinocyes


title: PBMCs, HF, 6

description: 10x Genomics


title: Monocytes, Heat4-encoding plasmid, rep4

description: Sample 8 - 15371

data_processing:
Resulting fastq reads were checked for quality using FastQC (version 0.11.9) and mapped against human reference GRCh38.p12 using hisat2 (version 2.1.0). SAM to BAM conversion and sorting was performed using samtools (version 1.10). Next, featureCounts (version 2.0.0) was applied to all BAM files for read counting using the –s2 option for reverse stranded libraries and the ENSEMBL Homo_sapiens.GRCh38.90.gtf. DESeq (version 1.36.0) was then used to generate FPKM counts.
Assembly: hg38
Supplementary files format and content: .txt-file containing FPKM counts

source_name: human primary monocytes (> 90% puritiy)

growth_protocol: Monocytes were isolated out of PBMCs by their size and density using a JE-5.0 counter-flow centrifugal elutriation system (Beckman Coulter, Brea, CA, USA) at 1,080 g centrifugal force. Size analysis and cell counts of the sorted cells were determined on a Beckman Coulter Z2 particle counter and size analyzer. Fractions containing more than 90% monocytes were used for further experiments.

extract_protocol:
Monocytes were harvested by centrifugation and washed with ice-cold PBS. RNA was purified from cells using the miRNeasy kit (Qiagen, #217004) according to manufacturer’s instructions with additional DNase (Qiagen, #79254) digestion.
Quality control and quantification of the isolated RNA were performed using Agilent fragment analyzer DNF-471 Standard Sensitivity RNA Kit. From each sample, 100 ng was used as input for library preparation using the Illumina Truseq totalRNA stranded Kit (#20020597). Ready prepped library was monitored again using the fragment analyzer and the DNF-473 Standard Sensitivity NGS Fragment Kit. Based on the measured concentration, libraries were then diluted to 5 nmol/l and equimolar amounts of each sample were plexed at 1.25 nmol/l. Sequencing was performed as paired-end 2 x 150 bp (S4-Flowcell) on a Novaseq 6000 (Illumina).

treatment_protocol: Monocytes were seeded in cell culture plates in RPMI-1640 medium (Merck, #R8758) supplemented with 10% fetal bovine serum (FBS; Gibco, #10500064) and Opti-MEM-PEI-plasmid mixture (3.5 ml Opti-MEM (ThermoFisher, #31985070), 7.5 µl PEI (Polysciences, #23966-1) and plasmid) was added. Monocytes were transfected with control (pcDNA) or Heat4-encoding plasmids for 24 h.

value: human primary monocytes (> 90% puritiy)

value: transfection with Heat4-encoding plasmid


title: PBMCs, HF, 4

description: 10x Genomics


title: CUT&RUN-HUSH, TASORKO, MPP8

value: TASOR KO


title: RNA-Seq Fat_progenitors_O_2

value: Visceral Fat

value: Fat progenitors


title: Monocytes, control plasmid (pcDNA), rep3

description: Sample 5 - 15365

value: transfection with control plasmid (pcDNA)


title: RNA-Seq Fat_progenitors_Y_3

value: 2 months


title: PBMCs, HF, 8

description: 10x Genomics


title: PBMCs, Control, 3

description: 10x Genomics


title: RNA-Seq Fat_progenitors_Y_2


title: A15_LFosL2_3_S12

source_name: mouse embryonic fibroblasts, Fra2 overexpression, day 10

value: mouse embryonic fibroblasts

value: C57/B16 background

value: Day 10


title: PBMCs, HF, 3

description: 10x Genomics


title: Monocytes, S100A9, RIP

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq were converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification. The fastq files underwent trimming and adapter removal using Trim Galore. Read mapping was performed against the hg19 reference genome using Bowtie2.
Gene expression quantification was achieved through read counting using FeatureCounts. The resulting counts were then converted to Fragments Per Kilobase Million (FPKM) for normalization in R.
bigWig files were generated using bamCoverage of deeptools.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Monocytes were lysed and RNA immunoprecipitation (RIP) was performed using the Magna RIP® RNA Binding Protein Immunoprecipitation Kit (Sigma-Aldrich, #17-700) according to manufacturer’s instructions. The following antibodies were used: normal rabbit IgG (Nordic Immunology, #RIgG), rabbit anti-S100A9 (0.328 µg; CellSignalling, #72590), rabbit anti-S100A8 (2 µg; ThermoFisher, #MA5-36007). RNA immunoprecipitation was validated by immunoblotting.
RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions. The RNA was fragmented at 94 °C for 15 minutes. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. Sequencing library was validated on the Agilent TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific). Sequencing libraries were multiplexed and clustered onto a flow cell on the Illumina NovaSeq instrument according to manufacturer’s instructions. Samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS).

treatment_protocol: x

value: S100A9 (Cell Signaling, #72590)


title: RNA-Seq Fat_progenitors_Y_1

data_processing:
Demultiplexed single end reads per sample here presented were mapped to the mouse GRCm38.p6/mm10 genome primary assembly using Spliced Transcripts Alignment to a Reference (STAR) software version 2.5.2b (Dobin et al. Bioinformatics 2013; https://doi.org/10.1093/bioinformatics/bts635). STAR was run with mode alignReads with parameters “--outFileterMatchMinOverLred 0.3 --outFilerScoreMinOverLread 0.3 --twopassMode Basic –sjdbGTFfile –quanMode GeneCounts”. Reads with duplicated UMIs were removed using the software Je version 2.0.RC option markdupes (Girardot et al. BMC Bioinformatics, 2016; https://doi.org/10.1186/s12859-016-1284-2). Transcript quantification was performed using featureCounts version 2.0.1 with parameters “–Q10 -M" (exonic regions of GENCODE’s vM24 annotation version) (Liao et al. NAR 2019; https://doi.org/10.1093/nar/gkz114).
Assembly: mm10
Supplementary files format and content: (.txt) counts

value: C57/Bl6 background


title: Monocytes, IgG, RIP

value: IgG (Nordic-Mubio, #RIgG)


title: Monocytes, siHeat4 + LPS, rep5

description: Sample 14 - SID14442, #12

treatment_protocol: SiRNA-mediated knockdown in human monocytes was performed via electroporation using the Neon™ Transfection System (ThermoFisher, #MPK10096). Monocytes were electroporated with siRNA in buffer T at 1900 V, 30 ms, 1 pulse. Transfected monocytes were transferred to RPMI-1640 medium (Merck, #R8758) supplemented with 10% fetal bovine serum (FBS; Gibco, #10500064) and cultured for 48 h at 37°C, 20% O2 and 5% CO2. Six hours before harvest, monocytes were treated with LPS (100 ng/ml; Sigma-Aldrich, #L5293). SiRNAs used: siSCR UCUCUCACAACGGGCAUUU[dT][dT], siHeat4 GGCUCACAUUCCGAUUGUUAU[dT][dT].

value: knockdown with siHeat4 + LPS treatment


title: RNA-Seq HSC_O_4

value: Bone Marrow

value: Hematopoietic stem cells

value: 22-24 months


title: Monocytes, control plasmid (pcDNA), rep4

description: Sample 7 - 15369

value: human primary monocytes (> 90% puritiy)


title: Monocytes, Heat4-encoding plasmid, rep3

description: Sample 6 - 15367

value: transfection with Heat4-encoding plasmid


title: A2_ENeg_2_S2

source_name: mouse embryonic fibroblasts, control, day 3

value: scrambled control

value: Day 3


title: RNA-Seq Fat_progenitors_O_3

value: Visceral Fat

value: Fat progenitors


title: Monocytes, Heat4-encoding plasmid, rep2

description: Sample 4 - 15359


title: A1_ENeg_1_S1


title: RNA-Seq Fat_progenitors_O_1


title: A7_EFosL2_1_S4


title: Monocytes, siHeat4, rep3

description: Sample 10 - SID14448, #13

value: knockdown with siHeat4


title: Monocytes, siSCR + LPS, rep4

description: Sample 11 - SID14439, #10

value: knockdown with siSCR + LPS treatment


title: Monocytes, siHeat4 + LPS, rep4

description: Sample 12 - SID14440, #10


title: A12_LNeg_3_S9

source_name: mouse embryonic fibroblasts, control, day 10

value: mouse embryonic fibroblasts

value: C57/B16 background


title: Monocytes, control plasmid (pcDNA), rep2

description: Sample 3 - 15357

value: transfection with control plasmid (pcDNA)


title: A11_LNeg_2_S8

value: Day 10


title: RNA-Seq CD8_Virtual_Mem_Y_5

value: Spleen

value: CD8 Virtual Memory

value: C57/Bl6 background

value: 2 months


title: Monocytes, control plasmid (pcDNA), rep1

description: Sample 1 - 15351


title: Monocytes, siHeat4 + LPS, rep2

description: Sample 8 - SID14446, #16

value: knockdown with siHeat4 + LPS treatment


title: PBMCs, HF, 2

description: 10x Genomics

value: HF patient

value: human PBMCs


title: Monocytes, siSCR + LPS, rep2

description: Sample 6 - SID14445, #16

value: human primary monocytes (> 90% puritiy)


title: RNA-Seq CD8_Virtual_Mem_Y_3


title: Monocytes, siSCR + LPS, rep5

description: Sample 13 - SID14441, #12


title: A14_LFosL2_2_S11


title: Monocytes, Heat4-encoding plasmid, rep1

description: Sample 2 - 15353

value: transfection with Heat4-encoding plasmid


title: RNA-Seq CD8_Virtual_Mem_Y_2


title: RNA-Seq CD8_Virtual_Mem_O_5

value: 22-24 months


title: RNA-Seq CD8_Virtual_Mem_Y_1


title: Monocytes, siSCR, rep3

description: Sample 9 - SID14447, #13

value: knockdown with siSCR


title: A13_LFosL2_1_S10


title: Monocytes, siSCR + LPS, rep1

description: Sample 2 - SID14443, #15


title: Monocytes, siHeat4 + LPS, rep1

description: Sample 4 - SID14444, #15


title: RNA-Seq CD8_Virtual_Mem_O_4


title: RNA-Seq CD8_Virtual_Mem_O_3


title: Monocytes, siSCR, rep2

description: Sample 5 - SID14451, #16


title: Monocytes, siSCR, rep1

description: Ssmple 1 - SID14449, #15


title: Monocytes, siHeat4, rep2

description: Sample 7 - SID14452, #16

value: knockdown with siHeat4


title: KASUMI2 - isolated from suspension replicate 2

city: Düsseldorf

first: Julian

last: Schliehe-Diecks

address: Moorenstr. 5

institute: Uniklinik Düsseldorf

description:
Kasumi_2_normalized_counts.txt
Kasumi_2_differentially_expressed_genes.txt

data_processing:
Adapters were trimmed with FASTQ Trimmer (11 bases of the 5' and 1 base of the 3')
Data quality was assesed via fastqc and aggregated with MultiQC
Reads were aligned to the hg38 reference genome via RNA STAR
Aligned reads were counted with featureCounts and aggregated into a count matrix
edgeR in combination with a gene annotation file was used to normalize the counts (log2 CPM) and to calculate the Fold Change and significance of the genes
Assembly: hg38
Supplementary files format and content: a tabular normalizied counts matrix
Supplementary files format and content: a tabular differentially expressed gene matrix

source_name: blood

growth_protocol: Leukemia cells and organoids were co-cultured in special organoid growth media: Base: 1:1 (v/v) DMEM/F12 and Neurobasal Medium (Gibco). Supplements: 1:200 (v/v) N2 supplement, 1:100 (v/v) B27 supplement (w/o) vitamin A, 1:100 L-glutamine, 0.05 mM nonessential amino acids (MEM) (Gibco), 100 U/mL penicillin, 100 μg/mL streptomycin, 1.6 g/L insulin (Sigma-Aldrich), 0.05 mM β-mercaptoethanol (Gibco), ALK5 inhibitor (5 μM) SB431542 (Selleckchem) and the AMPK pathway inhibitor (0.5 μM) Dorsomorphin (Sigma-Aldrich). Coculture duration was 14 days

extract_protocol:
Following the manufacturer's instructions, we used a Dynabeads™ CD19 Pan B (ThermoFisher) selection kit to isolate CD19+ cells from the organoid/leukemia cell suspension. The DETACHaBEAD CD19 kit (ThermoFisher) was used to separate beads from the suspension of positively isolated cells. RNA extraction was performed using the miRNeasy Micro Kit (50) #1071023 (Qiagen). The following cell quantities were isolated from 48 pooled organoids. For 697, we isolated 1.1 million cells from the organoids, and 0.4 million cells from the suspension. For Kasumi 2, we isolated 6.68 million from organoids, and 2.86 million cells from suspension. Flow cytometry analysis verified a 98% purity of CD19+ cells. Furthermore, automated cell counting indicated a viability exceeding 95% (Vi-Cell BLU, Beckman Coulter). Capillary gel electrophoresis was performed as a quality analysis and a 'Total RNA High Sensitivity Assay' (Agilent Technologies) on the FragmentAnalyzer System was implemented.
The library preparation was performed according to the manufacturer's protocol using the 'Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus' (Illumina Inc.) kit. Briefly, the following steps were performed: rRNA depletion, fragmentation, cDNA synthesis, adapter ligation and library amplification. Bead-purified libraries were normalized and sequenced on the NextSeq2000 system (Illumina Inc.) with a read setup of SR 1x101 bp.

treatment_protocol: Leukemia cells were not treated.

value: blood

value: B cell precursor leukemia

value: WT

value: Suspension


title: KASUMI2 - isolated from organoid replicate 3

value: invaded organoid


title: Monocytes, siHeat4, rep1

description: Sample 3 - SID14450, #15


title: Monocytes, control plasmid (pcDNA), S100A9, ChIP, rep4

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and demultiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification. Bowtie2 was used to align fastq reads to the hg38 human reference genome.
bigWig files were generated using bamCoverage of deeptools.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Monocytes were pelleted at 400 g at 4°C and washed with ice-cold PBS. Protein-protein interactions were cross-linked using 1.5 mM disuccinimidyl suberate (DSS; ThermoFisher, #21655), 1.5 mM ethylene glycol bis (EGS; ThermoFisher, #21565) and 1.5 mM disuccinimidyl glutarate (DSG; ThermoFisher, #20593) for 45 min in the dark with agitation at room temperature. ChIP was performed according to manufacturer’s instructions (Cell Signaling, #9005) with volumes adjusted for correct concentration during protein-DNA cross-linking. 1 µg of S100A9 antibody (Cell Signaling, #72590) or control IgG (Nordic-Mubio, #RIgG) were used per IP. Immunoprecipitation was validated by immunoblotting for S100A9 using a sample taken prior to chromatin elution from antibody/protein G magnetic beads.
After DNA purification (New England Biolabs, #T3010L) DNA libraries (Cell Signaling, #56795 & #47538) were prepped using equal volumes of eluted DNA. Library samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and library profiles were checked with DNA Kit on Agilent 5600 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). The sequencing libraries were multiplexed and loaded onto the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration. Image analysis and base calling were conducted by NovaSeq Control Software v1.6 on the NovaSeq instrument.

treatment_protocol: Monocytes were seeded in cell culture plates in RPMI-1640 medium (Merck, #R8758) supplemented with 10% fetal bovine serum (FBS; Gibco, #10500064) and Opti-MEM-PEI-plasmid mixture (3.5 ml Opti-MEM (ThermoFisher, #31985070), 7.5 µl PEI (Polysciences, #23966-1) and plasmid) was added. Monocytes were transfected with control (pcDNA) or Heat4-encoding plasmids and treated with IL-10 (100 ng/ml; R&D Systems, #1064-ILB-050) for 24 h.

value: transfection with control plasmid (pcDNA)

tag: chip antibody

value: S100A9 (Cell Signaling, #72590)


title: KASUMI2 - isolated from suspension replicate 1


title: Monocytes, Heat4-encoding plasmid + IL-10, IgG, ChIP, rep4

value: transfection with Heat4-encoding plasmid + IL-10 treatment

value: IgG (Nordic-Mubio, #RIgG)


title: RNA-Seq CD8_Virtual_Mem_O_2

extract_protocol:
RNA-seq
Poly-A based RNA sequencing libraries were generated as described by us (Sun et al.  Nat Comms 2021;  https://doi.org/10.1038/s41467-021-22863-0.). In brief, a 3-prime biased approach was used to generate sequencing libraries. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template-switching oligonucleotide. The Illumina P5 (5′-AAT GAT ACG GCG ACC ACC GA-3′) and P7 (5′-CAA GCA GAA GAC GGC ATA CGA GAT-3′) sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilises a custom primer (5′-GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C-3′) to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification.
For RNA sequencing, a 3-prime biased approach was used to generate sequencing libraries as described previously (Sun et al.  Nat Comms 2021;  https://doi.org/10.1038/s41467-021-22863-0.). Barcoded 19bp R1 and 111bp R2 paired-end reads per sequencing lane were assigned to individual samples using the sabre software (version 80faf94) with options “-u –m2 –l 10’ (https://github.com/najoshi/sabre) (Tsyganov et al. JOSS 2018; https://doi.org/10.21105/joss.00583).

value: Spleen

value: CD8 Virtual Memory

value: C57/Bl6 background


title: RNA-Seq CD8_Virtual_Mem_O_1


title: KASUMI2 - isolated from suspension replicate 3


title: Monocytes, control plasmid (pcDNA), IgG, ChIP, rep4

value: human primary monocytes (> 90% puritiy)


title: Monocytes, Heat4-encoding plasmid + IL-10, S100A9, ChIP, rep4


title: A10_LNeg_1_S7

value: mouse embryonic fibroblasts

value: C57/B16 background

value: scrambled control

value: Day 10


title: KASUMI2 - isolated from organoid replicate 2

value: blood


title: Monocytes, Heat4-encoding plasmid + IL-10, S100A9, ChIP, rep3


title: RNA-Seq CD8_Naive_Y_4

value: CD8 Naive

value: 2 months


title: RNA-Seq CD8_Virtual_Mem_Y_4


title: Monocytes, Heat4-encoding plasmid + IL-10, IgG, ChIP, rep3


title: KASUMI2 - isolated from organoid replicate 1

value: B cell precursor leukemia

value: WT


title: Monocytes, control plasmid (pcDNA), S100A9, ChIP, rep3

value: transfection with control plasmid (pcDNA)


title: Monocytes, control plasmid (pcDNA), IgG, ChIP, rep3


title: RNA-Seq CD8_Naive_Y_3


title: 697 - isolated from suspension replicate 3

description:
697_differentially_expressed_genes.txt
697_normalized_counts.txt

value: Suspension


title: Monocytes, Heat4-encoding plasmid + IL-10, S100A9, ChIP, rep2

value: transfection with Heat4-encoding plasmid + IL-10 treatment

value: S100A9 (Cell Signaling, #72590)


title: RNA-Seq CD8_Naive_Y_2

value: Spleen


title: Monocytes, Heat4-encoding plasmid + IL-10, IgG, ChIP, rep2

value: IgG (Nordic-Mubio, #RIgG)


title: Monocytes, control plasmid (pcDNA), S100A9, ChIP, rep2


title: 697 - isolated from suspension replicate 2


title: Monocytes, control plasmid (pcDNA), IgG, ChIP, rep2


title: RNA-Seq CD8_Naive_O_3

value: C57/Bl6 background

value: 22-24 months


title: Monocytes, Heat4-encoding plasmid + IL-10, S100A9, ChIP, rep1

value: human primary monocytes (> 90% puritiy)


title: Monocytes, Heat4-encoding plasmid + IL-10, IgG, ChIP, rep1


title: Monocytes, control plasmid (pcDNA), S100A9, ChIP, rep1


title: Monocytes, control plasmid (pcDNA), IgG, ChIP, rep1


title: RNA-Seq CD8_Naive_O_2


title: 697 - isolated from organoid replicate 3

value: invaded organoid


title: 697 - isolated from organoid replicate 2


title: RNA-Seq CD8_Naive_O_1


title: M07e_JAK3Q988P_PIM447_biol rep 1

city: Madrid

first: Maria

last: Villa-Morales

email: maria.villa@uam.es, mvilla@cbm.csic.es

state: Madrid

address: Nicolas Cabrera 1

country: Spain

institute: UNIVERSIDAD AUTONOMA DE MADRID

data_processing:
Paired-end sequencing (2x100bp) of the previously enriched, indexed and multiplexed libraries were performed on the high-throughput NovaSeq 6000 platform (Illumina Inc.), with a minimum of 100M PE reads (50+50) per sample, with a read quality of 85%>Q30. For bioinformatics analysis, GRCh38/hg38 (Ensembl version 103) genome was used as a reference. Briefly, quality check and sequence trimming were performed using FASTQC and fastp5 respectively. Then, the trimmed RNA-seq reads were aligned against the reference genome and the transcripts were assembled using HISAT2 tool6. Corresponding genes were obtained and their expression abundance was determined using StringTie suite (https://ccb.jhu.edu/software/stringtie/). On gene counting matrices, reads were subjected to unsupervised filtering in order to discard those genes with very few or no reads throughout all the samples of the study (https://bioconductor.org/packages/release/bioc/html/genefilter.html). Genes with a total abundance below 15 reads were excluded from further analysis.
Assembly: GRCh38/hg38,  Ensembl version 103
Supplementary files format and content: csv file with raw counts of sequencing reads for each sample

source_name: peripheral blood

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quantification and quality were checked by Nanodrop (Thermo Fisher Scientific Inc.), Qubit (Thermo Fisher Scientific Inc) and TapeStation (Agilent Technologies).
Using the TruSeq Stranded Total RNA Library Prep (Illumina, Inc.) and included rRNA depletion, fragmentation, cDNA synthesis and adaptor ligation. The generated libraries were normalized and combined in equimolecular concentrations for optimal generation of DNA clusters.

value: peripheral blood

value: M07e cell line

value: acute megakaryoblastic leukemia

value: expressing JAK3 Q988P

value: treated with 1 µM PIM447 (Selleckchem #LGH44) for 24h


title: M07e_JAK3Q988P_PIM447_biol rep 2


title: 697 - isolated from organoid replicate 1

value: blood

value: B cell precursor leukemia


title: RNAseq-DOX-OHT-N3

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

description: RNA-seq

data_processing:
Basecalls were performed using bcl2fastq v1.1.0 (Illumina) and the quality of the generated FASTQ files was analysed with FastQC.
For mRNA sequencing, reads were aligned to the human genome (hg19/GRCh37) using STAR aligner v2.7.9a with default parameters and gene quantification (--quantMode GeneCounts). The output table with teh gene counts was futher analyzed in R v4.1.1 and processed with DESeq2 package according to the manual. Genes with at least 15 counts in at least 3 samples were kept in the counttable. All samples were then normalized by size factors.
Following read-normalization, the fold average for 3 independent biological replicates (N1, N2, N3) was calculated on treatment to control. Where applicable, the calculated fold-changes were averaged in 100 genes per bin for a total of 140 bins of 14085 genes.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file that includes the raw-counts for all 12 individual samples in a singel table. This count-table was used to carry out all further data-processing steps as outlined above.

source_name: SH-EP NMYC-ER

growth_protocol: Human neuroblastoma derived SH-EP cells expressing an exogenous and 4-OHT inducible NMYC allele (SH-EP-NMYC-ER), were grown in RPMI-1640 medium supplemented with with 10% horse serum and 1% penicillin/ streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For RNA sequencing, cells were harvested and total RNA was extracted with RNeasy MiniKit (Qiagen) according to manufacturer's instructions. On-column Dnase I digestion was performed followed by mRNA isolation with the NEBNext Poly(A) mRNA Magnetic Isolation Kit (NEB).
Library preparation was done with the NEBNext Ultra II Directional RNA Library Prep for Illumina (NEB) following the manufacturer's manual. Libraries were size-selected using SPRIselect beads (Backman-Coulter) after amplification with 9 PCR cycles using the NEBNext Multiplex Oligos for Illumina Kit (NEB). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Sequencing was performed in paired-end mode on a NextSeq2000 platform (Illumina).

treatment_protocol: The indcution of NMYC in the SH-EP-NMYC-ER cells was achieved by adding 4-OHT (200 nM) for 4 hours. The expression of an shRNA targeting TF3C5 in the SHEP-NMYCER cells was induced with 1 µg/ml doxycycline for 48 hours.

value: SH-EP NMYC-ER

value: Neuroblastoma

tag: dox-treatment (shrna-tf3c5)

value: induced (shRNA expression)

tag: 4-oht treatment_(nmyc_expresion)

value: induced (NMYC expression)

tag: treatment with_inhibitor

value: not applicable

tag: biological replicate


title: RNA-Seq CD8_Memory_Y_3

value: Spleen

value: CD8 Memory

value: 2 months


title: M07e_JAK3Q988P_untreated_biol rep 3

value: untreated


title: RNA-Seq CD8_Memory_Y_4

value: C57/Bl6 background


title: M07e_JAK3Q988P_untreated_biol rep 2

value: peripheral blood


title: M07e_JAK3Q988P_untreated_biol rep 1

value: M07e cell line


title: RNAseq-DOX-EtOH-N3

description: RNA-seq

value: uninduced (no NMYC expression)


title: M07e_untransduced_biol rep 2

value: acute megakaryoblastic leukemia

value: untransduced


title: RNA-Seq CD8_Naive_Y_1

value: CD8 Naive


title: RNAseq-EtOH-OHT-N3

description: RNA-seq

value: uninduced (no shRNA expression)


title: 697 - isolated from suspension replicate 1

value: blood

value: B cell precursor leukemia

value: WT

value: Suspension


title: RNA-Seq CD8_Memory_Y_2


title: M07e_untransduced_biol rep 3


title: M07e_untransduced_biol rep 1


title: RNA-Seq CD8_Memory_O_3

value: 22-24 months


title: RNA-Seq CD8_Memory_O_2

value: Spleen