title: Macrophages, 2 Hypoxia Edicotinib

value: Hypoxia


title: BV2 cells, Radiation+5α-androst-3β, 5α, 6β-triol  [Y3]

status: Public on Apr 18 2024

type: SRA

city: Guangzhou

first: Yamei

last: Tang

state: Guangdong

address: 107 Yan Jiang West Road

department: Department of Neurology

country: China

institute: Sun Yat-Sen Memorial Hospital

library_source: transcriptomic

data_processing:
Clean data were filtered from the reads obtained from the sequencing machines with fastp (version 0.18.0) using the following parameters: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
The clean reads were quality controlled with FastQC and aligned to the mouse genome GRCm38 with STAR (version 2.7.1a) using the default parameters.
After the alignment, the reads were quantified to gene level with featureCounts from Subread (version 1.6.3) using the Ensembl annotation (GRCm38, release 96).
The read counts of genes were used for further analysis.
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include feature counts for each Sample

molecule: total RNA

organism: Mus musculus

growth_protocol: The immortalized murine microglia BV2 cells were cultured in DMEM/F12 medium supplemented with penicillin and streptomycin and 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted using Trizol reagent kit according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer's protocol.

treatment_protocol: BV2 cells were pretreated with 10µM 5α-androst-3β, 5α, 6β-triol or vehicle (20% HP-β-CD) for 30 minutes before a single dose of 10Gy X-ray radiation.

tag: tissue

value: brain

tag: cell line

tag: cell type

value: immortalized murine microglia

tag: genotype

value: WT

tag: treatment

value: Radiation+5α-androst-3β, 5α, 8β-triol


title: BV2 cells, Radiation+5α-androst-3β, 5α, 6β-triol  [Y2]

value: Radiation+5α-androst-3β, 5α, 7β-triol


title: Macrophages, 2 Hypoxia Vehicle

city: La Tronche

first: arnaud

last: MILLET

address: Allée des Alpes

country: France

institute: Institute for Advanced Studies

data_processing:
Gene expression was performed using the STAR software
Assembly: hg38
Supplementary files format and content: tab delimited-text files includes raw counts for each samples

organism: Homo sapiens

source_name: Monocytes derived macrophages

extract_protocol:
RNA extraction was performed using the Nucleospin RNA kit (Macherey Nagel)
RNA library for RNAseq was prepared using the kit NEBNext Ultra II mRNAseq

tag: group

value: Monocytes derived macrophages

tag: stress

value: Vehicle


title: BV2 cells, Radiation+5α-androst-3β, 5α, 6β-triol  [Y1]

value: Radiation+5α-androst-3β, 5α, 6β-triol


title: Donor.D932_DARIC33_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

country: USA

institute: Regeneron

description:
Two technical replicates of 150bp PE
F9

data_processing:
Reads were filtered for quality and aligned to the Genome Resource Consortium hg38 human genome reference using STAR (2.6.1d).
Gene expression was quantified as transcripts per million (TPM) using RSEM (1.3.1).
Assembly: hg38
Supplementary files format and content: comma-delimited text file contains RSEM TPMs for each sample.
Supplementary files format and content: comma-delimited text file contains RSEM expected counts for each sample.

source_name: CD4+ T cells

growth_protocol: To generate research scale DARIC cell products, PBMCs were thawed (recorded as day 0 of culture) and resuspended in TCGM supplemented with 250 IU/ml recombinant human IL-2 (Stemcell, catalog 78220.3) prior to activation with 50ng/ml anti-CD3 (clone OKT3) and anti-CD28 (clone 15E8) antibodies (Miltenyi Biotec). Lentivirus supernatants were directly added to PBMC cultures 24 hours later (multiplicity of infection [MOI] = 10). On day 3 of culture (72 hours after activation), transduced PBMC were collected, washed, and resuspended in complete TCGM with human IL-2 at 0.5 x 10^6 cells/ml and transferred to gas permeable culture vessels (G-REX, WilsonWolf). PBMC cultures were expanded in vitro at cell density of 0.5-2 x 10^6 cells/ml maintained by the addition of fresh media every 2-3 days for a total of 10-11 days until cryopreservation.

extract_protocol:
Total RNA was isolated using the Qiagen 96-well RNeasy Prep Kit.
Libraries were generated using KAPA 148 Hyperprep Kit with RiboErase and KAPA Unique Dual-Indexed Adapter Kit (Roche).
The sequencing strategy was two technical replicates of 150bp paired-end reads.  Samples were sequenced on a NextSeq500 instrument.

treatment_protocol: DARIC33 T cells and untransduced T cells generated from four donor PBMC samples were cultured with media or media supplemented with 1 nM rapamycin for 24 hours, washed and then stimulated with MV4-11 tumor cells or left unstimulated for an additional 24 hours. Cells were then sorted into CD4+ and CD8+ populations using a FACSAria (BD Biosciences).  In addition, transcriptomes were assesed at the 168hr timepoint for CD4+ and CD8+ DARIC33 transduced T cells derived from 3 donors and incubated with 1nM rapamycin and activated by CD33+ MV4-11 AML target cells.

value: CD4+ T cells

tag: transgene

tag: donor

value: 1nM rapamycin

tag: stimulation

value: CD33+ MV4-11 AML target cells

tag: time


title: Flag_MBD2c+NTC

city: Hefei

first: Yijie

last: Hao

address: Huangshan Road 443

institute: USTC

library_source: genomic

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format, which contains sequence information.
Quality control is applied to guarantee the meaningful downstream analysis, and  fastp (version 0.23.1) is used to perform basic statistics on the quality of the raw reads.
Sequenced reads were mapped to the hg19 ChM only using software Bowtie2 (version 2.2.6). Aligned reads were used for subsequent generation of bindingprofiles, peak callings, motif analyses and traveling ratio analyses.
Assembly: hg19 ChM
Supplementary files format and content: bw for ChIP-seq data

molecule: genomic DNA

source_name: human breast cancer

growth_protocol: DMEM supplemented with 10% FBS and 1% Pen/Strep. Cells were maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde and subsequently quenched with 0.125 M glycine. The cells were sonicated using a Scientz JY99-IIDN device. Anti-Flag antibody (Sigma-Aldrich) were used.
The DNA fragments were end-repaired and A-tailed, which were further ligated with sequencing adaptors. The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution by Agilent 5400 system(Agilent, USA) and quantified by qPCR (1.5 nM).

treatment_protocol: shRNAs targeting TFAM were commercially purchased (Sigma-Aldrich). Flag- MBD2c were cloned into pSin-3xFlag  vectors.

value: human breast cancer

value: MDA-MB-468 infected with viruses expressing  Flag-MBD2c and NTC using Flag antibody (Sigma-Aldrich, Cat#F1804) to IP genomic DNA.


title: Macrophages, 2 Normoxia Edicotinib

value: Normoxia

value: Edicotinib


title: Donor.D1173_Untransduced_CD4_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
D9

value: Untransduced

value: media alone


title: Donor.D2172_Untransduced_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
E9


title: BV2 cells, Radiation+vehicle [R2]

source_name: BV2 cells, Radiation+vehicle

value: brain

value: Radiation+vehicle


title: BV2 cells, Radiation+vehicle [R3]

value: immortalized murine microglia

value: WT


title: Donor.D2172_Untransduced_CD8_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
B9

source_name: CD8+ T cells

value: CD8+ T cells


title: Donor.D1173_DARIC33_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
A9


title: Macrophages, 1 Hypoxia Edicotinib

value: Monocytes derived macrophages

value: Hypoxia


title: BV2 cells, Radiation+vehicle [R1]


title: BV2 cells, Control+vehicle [C3]

source_name: BV2 cells, Control+vehicle

value: vehicle


title: ctrl-2

city: Shanghai

first: ZHU

middle: JIA

last: YAN

address: 197 Ruijin Er Rd

institute: Department of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava software used for basecalling.
Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted );Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality);Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

growth_protocol: EL4 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)  with 10% HBS, 2 mM L-glutamine, and antibiotics  in a humidified atmosphere containing 5% CO2 at 37°C

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNALibrary Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’srecommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 10μM RGFP966 (Abmole) or vehicle were added to the cell culture medium 24 hr in advance

value: T lymphocyte cells


title: Macrophages, 1 Hypoxia Vehicle

value: Vehicle


title: Macrophages, 1 Normoxia Edicotinib


title: Macrophages, 1 Normoxia Vehicle


title: BV2 cells, Control+vehicle [C1]


title: BV2 cells, Control+vehicle [C2]


title: Donor.D2172_Untransduced_CD8_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
D8

value: 1nM rapamycin

value: Unstimulated


title: primary keratinocytes, siSNHG7-48h-B

city: London

first: Matteo

last: Vietri Rudan

address: Great Maze Pond

department: Centre for Gene Therapy and Regenerative Medicine

country: United Kingdom

institute: King's College London

description:
siSNHG7-48h-B
siScr48-siSNHG748h_DE_analysis.csv

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes.
Assembly: GRCh38
Supplementary files format and content: Processed data files report gene expression differences between control and knockdown cells at 24 and 48h post transfection. Files are in .csv format

source_name: Primary keratinocytes

extract_protocol:
Total RNA extraction
rRNA depletion; RNA fragmentation and random priming; first and second strand cDNA synthesis; end repair, 5' phosphorylation, and dA-tailing; adaptor ligation, PCR enrichment, and sequencing
Illumina NovaSeq, PE 2x150

value: Primary keratinocytes

value: 48h post-transfection


title: primary keratinocytes, siSNHG7-48h-A

description:
siSNHG7-48h-A
siScr48-siSNHG748h_DE_analysis.csv


title: Donor.D1173_DARIC33_CD8_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
B8


title: Donor.D1173_DARIC33_CD4_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
C9

value: CD4+ T cells


title: PB_classical monocytes,SF3B1wt LR-MDS, patient 2

city: Dresden

first: Susann

last: Winter

address: Fetscherstrasse 74

country: Germany

institute: University Hospital Carl Gustav Carus, Faculty of Medicine Carl Gustav Carus, TU Dresden

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into FASTQ files and de-multiplexed using Illumina’s bcl2fastq Conversion Software v2.20. Sequencing quality of raw FASTQ files was checked using FastQC 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter trimming and quality filtering of sequence reads were performed using Seqtk and cutadapt. The adapter clipped reads were also aligned to ribosomal RNA sequences using Bowtie 2 (v2.4.1) and the mapped reads were discarded. After that, mapping against the human genome (GRCh38 version 32 [Ensembl 98]) was performed using STAR aligner v.2.7.9a.
The R package EBSeq was used for normalization and to infer differential gene and isoform expressions.
Assembly: GRCh38 version 32/Ensembl 98
Supplementary files format and content: Table containing normalized counts for biological replicates

source_name: PBMCs

growth_protocol: Monocytes (195000 – 500000 cells per 96-well in 250 µl RPMI 1640/PenStrep/5% heat-inactivated human serum) were cultivated for 4 hours in humidified atmosphere (5% CO2, 37°C).

extract_protocol:
RNA was isolated with TRIzol and Direct-zol™ RNA Microprep
Ultra-low input RNA sequencing library was prepared by using SMART-Seq HT kit for full-length cDNA synthesis and amplification (Takara, San Jose, CA, USA), and Illumina Nextera XT (Illumina, San Diego, CA, USA) was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
RNA-seq, 2x150 bp paired-end configuration

tag: disease

value: LR-MDS

value: PBMCs

value: classical monocytes (CD14+ CD16-)

tag: gender

value: male

value: SF3B1wt, EZH2mut, CBLmut


title: PB_classical monocytes,SF3B1wt LR-MDS, patient 1

value: SF3B1wt, PHF6mut, TET2mut


title: Mutant strain, iron deplete, 90 minutes, replicate 2

city: East Lansing

first: Srinand

last: Sreevatsan

state: MI

address: 784 WILSON RD

department: Pathobiology and Diagnostic investigation

institute: Michigan State University

data_processing:
All reads were checked for QC using FastQC (version 0.11.7) to visualize the quality of the reads using HPCC clusters.
Reads were processed using Trimmomatic tool to trim adaptor sequences/ low quality sequences using HPCC clusters.
Trimmed reads were mapped to reference genome (MAP K-10) using HISAT2. Reads counts were generated using HTSeq.
Assembly: MAP K-10 (Genbank accession number: NC_002944.2)
Supplementary files format and content: compressed gzip fastq files includes raw reads for each sample
Supplementary files format and content: tab-delimited text file include Normalised counts for each sample and replicates

organism: Mycobacterium avium subsp. paratuberculosis

source_name: MAP3773c deletion strain

growth_protocol: Both strains were grown and maintained at 37°C in Middlebrook 7H9 broth supplemented with 10% OADC (oleic acid, dextrose, catalase); 0.05% Tween 80 and 2 mg/ml of ferric mycobactin J.

extract_protocol:
Total RNA was extracted using Trizol reagent followed by adding cholorform followed by centrifugation. The upper aqueous phase was added to a new microcentrifuge tube containing 100% RNase free ethanol which was then processed by Qiagen RNeasy kit DNase treatment and finally with the Ambion Turbo DNA-free kit.
RNA-Seq libraries were prepared using the mRNA Seq paired end read library preparation kit

treatment_protocol: Iron starvation was accomplished by treating cultures with DIP (200μM final) for 5, 30, 60, and 90 minutes shaken at 200rpm at 37°C

tag: strain

value: MAP3773c deletion strain

tag: treatment/time

value: Iron restriction post 90 minutes


title: Mutant strain, iron deplete, 90 minutes, replicate 1


title: Macrophages, 2 Normoxia Vehicle

value: Monocytes derived macrophages

value: Normoxia


title: Donor.D732_DARIC33_CD8_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
C8

value: CD8+ T cells

value: media alone

value: CD33+ MV4-11 AML target cells


title: Donor.D2172_Untransduced_CD4_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
A8

value: Untransduced


title: Mutant strain, iron deplete, 60 minutes, replicate 2

value: Iron restriction post 60 minutes


title: primary keratinocytes, siSNHG7-24h-B

description:
siSNHG7-24h-B
siScr24h-siSNHG724h_DE_analysis.csv

value: Primary keratinocytes

value: 24h post-transfection


title: PB_classical monocytes,SF3B1K700E LR-MDS, patient 3

value: LR-MDS


title: All samples

city: San Francisco

first: Tatsuya

last: Tsukui

state: CA

address: 555 Mission Bay Blvd South, 282

department: Medicine

institute: UCSF

library_source: transcriptomic single cell

data_processing:
Fastq files were uploaded to 10x Genomics cloud analysis website (https://www.10xgenomics.com/products/cloud-analysis) and reads were aligned to a custom reference of mouse genome mm10 with tdTomato-WPRE-polyA transcript sequence.
The data were demultiplexed and multiplets identified by the presence of multiple oligonucleotide tags were removed using 10x Genomics cloud analysis function with default parameters.
Raw count matrices were imported to the R package Seurat v4.1.0 and cells with fewer than 200 detected genes, larger than 7500 detected genes, or larger than 15% percent mitochondria genes were excluded.
We used DoubletFinder package for individual samples to remove doublets that were not detected upon alignment using estimated multiple rate 2%.
We then merged all the sample objects by RunFastMNN
Assembly: mm10 with tdTomato-WPRE-polyA
Supplementary files format and content: rds file: Seurat v4 object after filtering, merging, and clustring
Supplementary files format and content: mtx, tsv, csv files: raw count, barcode, genes, and meta data before any filtering

source_name: Lung

extract_protocol:
Lungs were harvested and dissociated by collagenase and dispase at 37C for 60 min. Mesenchymal cells (CD31-, CD45-, EpCAM-, Ter119-) were enriched by magnetic negative selection and FACS.
Three biological replicates at each time point were multiplexed by 10x Genomics 3’ CellPlex Kit.  Tag assignment was as follows; day 0 (301, 302, 303), day 7 (304, 305, 306), day 14 (307, 308, 309), and day 21 (310, 311, 312). All 12 samples were pooled and 30,000 cells / lane were loaded onto 4 lanes of Chromium Next GEM Chip (10x Genomics). Chromium Single Cell 3’ v3.1 (10x Genomics) reagents were used for library preparation

treatment_protocol: Sucbe2-CreER/Rosa26-tdTomato double homozygous mice were treated with 2mg tamoxifen/day for two weeks. Two weeks after the last tamoxifen injection, mice were treated with 2.5U/kg bleomycin by oropharyngeal aspiration, and harvested on day 0 (non-bleomycin treated), 7, 14, and 21

value: Lung

value: Mesenchymal cells

value: Scube-CreER +/+, Rosa26 tdTomato/tdTomato

value: non-bleomycin-treated or bleomycin treated


title: Donor.D932_Untransduced_CD4_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
F7

value: CD4+ T cells

value: Unstimulated


title: primary keratinocytes, siScramble-48h-B

description:
siScr-48h-B
siScr48-siSNHG748h_DE_analysis.csv

value: 48h post-transfection

value: siScramble


title: Mutant strain, iron deplete, 60 minutes, replicate 1

value: MAP3773c deletion strain


title: PB_classical monocytes,SF3B1K700E LR-MDS, patient 2

value: PBMCs

value: classical monocytes (CD14+ CD16-)

value: male


title: Donor.D732_Untransduced_CD4_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
F8

value: Untransduced

value: media alone

value: CD33+ MV4-11 AML target cells


title: primary keratinocytes, siScramble-48h-A

description:
siScr-48h-A
siScr48-siSNHG748h_DE_analysis.csv

value: Primary keratinocytes


title: Donor.D932_Untransduced_CD4_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
E7

value: 1nM rapamycin


title: Donor.D732_Untransduced_CD8_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
E8

value: CD8+ T cells


title: primary keratinocytes, siScramble-24h-B

description:
siScr-24h-B
siScr24h-siSNHG724h_DE_analysis.csv

value: 24h post-transfection


title: PB_classical monocytes,SF3B1K700E LR-MDS, patient 1

value: LR-MDS


title: Donor.D2172_DARIC33_CD8_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
D7


title: Mutant strain, iron deplete, 30 minutes, replicate 2

value: Iron restriction post 30 minutes


title: PB_classical monocytes,SF3B1wt LR-MDS, patient 3

value: SF3B1wt, ZRSR2mut, TET2mut


title: primary keratinocytes, siScramble-24h-A

description:
siScr-24h-A
siScr24h-siSNHG724h_DE_analysis.csv


title: Mutant strain, iron deplete, 30 minutes, replicate 1


title: primary keratinocytes, siSNHG7-24h-A

description:
siSNHG7-24h-A
siScr24h-siSNHG724h_DE_analysis.csv


title: PB classical monocytes, healthy donor 3

value: HD

value: female

value: healthy donor


title: Donor.D932_DARIC33_CD4_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
C7

value: CD4+ T cells


title: PB classical monocytes, healthy donor 2

value: PBMCs


title: PB classical monocytes, healthy donor 1

value: classical monocytes (CD14+ CD16-)


title: Donor.D932_DARIC33_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_168h

description:
Two technical replicates of 150bp PE
A7


title: Mutant strain, iron deplete, 5 minutes, replicate 2

value: MAP3773c deletion strain

value: Iron restriction post 5 minutes


title: OE-3

city: beijing

first: min

last: Fu

address: Peking University School and Hospital of Stomatology, No.22, Zhongguancun South Avenue, Haidian District

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and 1ow quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow: $$FPKM = {cDNA Fragments lover (Mapped Fragments (Mi11ions）* TranscriptLength (kb)}}$$
Assembly: GRCh38
Supplementary files format and content: list file includes FPKM values for each Sample

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen, USA), according to the manufacturer's instructions
mRNA was purified, fragmented, and converted to cDNA, followed by adaptor ligation, size selection, and PCR amplification to generate sequencing libraries using the NEBNext UltraTM RNA Library Prep Kit for Illumina.

value: salivary adenoid cystic carcinoma cells

value: circMYBL3 overexpression


title: Donor.D2172_DARIC33_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_168h

description:
Two technical replicates of 150bp PE
F6

value: CD33+ MV4-11 AML target cells


title: OE-1

institute: Peking University School and Hospital of Stomatology

value: circMYBL1 overexpression


title: Vec-3

value: WT


title: Donor.D732_DARIC33_CD8_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
E6

value: CD8+ T cells

value: media alone

value: Unstimulated


title: Mutant strain, iron replete, replicate 1

value: No iron restriction- control


title: SUNE-1  cells, KLF5, ChIP

first: zhenyu

last: yang

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

data_processing:
ChIP-seq reads were filtered and quality-verified using SOAPnuke program (v.2.0).
ChIP-seq reads were aligned to the hg38 genome assembly using SOAP2  version 2.21
Peaks were called using model-based MACS2 software (v.2.1.1) and annotated with the closest hg38 genes by annotatePeaks of HOMER (v.4.11).
Assembly: hg38
Supplementary files format and content: wig files

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. After quenching, lysates were clarified from sonicated nuclei.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: nasopharyngeal carcinoma cells

tag: chip antibody

value: KLF5(Sigma-Aldrich, 09822)


title: K-10, iron deplete, 90 minutes, replicate 2

source_name: MAP K-10- Parent strain

value: MAP K-10- Parent strain

value: Iron restriction post 90 minutes


title: Quadriceps muscle, Thbs1_transgenic_2

city: Cincinnati

first: Jeffery

middle: D

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Assembly: mm10
Supplementary files format and content: Excel file represents raw counts with genes in rows and samples in columns

source_name: Quadriceps muscle

growth_protocol: Six to eight week old mice were euthanized and quadriceps muscle immediately harvested for processing

extract_protocol:
Total RNA from control and transgenic muscle was isolated using standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skeletal muscle

value: FVB/N

value: Thbs1 overexpression


title: SUNE-1 cells, input

value: IgG(Thermo Fisher Scientific)


title: Donor.D932_DARIC33_CD8_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
D6


title: Vec-2

value: salivary adenoid cystic carcinoma cells


title: Vec-1


title: K-10, iron deplete, 90 minutes, replicate 1


title: K-10, iron deplete, 60 minutes, replicate 2

value: Iron restriction post 60 minutes


title: Quadriceps muscle, Non_transgenic control_2

value: control


title: Mutant strain, iron replete, replicate 2

value: MAP3773c deletion strain


title: HK1 cells, input

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version 0.20.1).
Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. The clean reads were mapped to the genome using bowtie2(version 2.4.2). MACS2(version 2.2.7.1) was used to call peaks.
Called peaks were then annotated using R package ChIPseeker.
Assembly: hg19
Supplementary files format and content: bigwig files


title: Donor.D732_DARIC33_CD4_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
B7

value: CD4+ T cells


title: Donor.D1173_Untransduced_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
B6

value: Untransduced

value: 1nM rapamycin

value: CD33+ MV4-11 AML target cells


title: Mutant strain, iron deplete, 5 minutes, replicate 1

value: Iron restriction post 5 minutes


title: Donor.D1173_DARIC33_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_168h

description:
Two technical replicates of 150bp PE
A6

value: CD8+ T cells


title: K-10, iron deplete, 30 minutes, replicate 2

value: Iron restriction post 30 minutes


title: C666-1 cells, input

value: nasopharyngeal carcinoma cells


title: HK1  cells, KLF5, ChIP

value: KLF5(Sigma-Aldrich, 09822)


title: Quadriceps muscle, Thbs1_transgenic_1

value: skeletal muscle


title: HFDBA_Sham_b

city: Shenzhen

first: jianhui

last: liang

address: 1068 Xueyuan Avenue, Nanshan District

institute: Shenzhen Institute of Science and Technology

data_processing:
Raw sequencing reads (fastq) were quality checked using SOAPnuke (v1.5.2).
Bowtie2 (v2.2.5) was applied to align the clean reads to the genomes.
The expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using DESeq2 (v1.4.5)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: core_table_gene2.xls

source_name: synovial membrane

growth_protocol: Mice were  fed with regular diets

extract_protocol:
RNAs were extracted from synovial membrane. The samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: To further investigate whether obesity influences RA, we established collagen-induced-arthritis (CIA) models in mice using both regular and high-fat diets (HFD), and collected synovial tissue and performed RNA sequencing.

value: synovial membrane

value: sham

value: high-fat diets (HFD)


title: HFDBA_Sham_a


title: Donor.D2172_DARIC33_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_168h

description:
Two technical replicates of 150bp PE
F5


title: C666-1  cells, KLF5, ChIP


title: Donor.D932_Untransduced_CD8_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
D5

value: media alone


title: Donor.D932_DARIC33_CD8_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
C6

value: Unstimulated


title: HFDBA_CIA_c

value: collagen-induced-arthritis (CIA)


title: K-10 , iron deplete, 5 minutes, replicate 2

value: MAP K-10- Parent strain


title: H9-6h-2

data_processing:
Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system
After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing. Commonly, the lncRNA-seq use PE150 (paired-end 150nt) sequencing.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5; At the same time, Q20, Q30 and GC content of the clean data were calculated. Then, map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecount was used to count the reads numbers mapped to each gene.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: H9  cells were cultured in RPMI 1640 (C11875500, Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS) (10270-106, Gibco, Carlsbad, CA, USA), 2 mM L-glutamine, and antibiotics

extract_protocol:
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 0.05μM doxorubicin were added to the cell culture medium 6 hr in advance

value: T lymphocyte cells

value: WT

value: doxorubicin for 6 hours


title: Donor.D932_Untransduced_CD8_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
E5

value: Untransduced


title: HFDBA_CIA_b


title: K-10, iron deplete, 60 minutes, replicate 1

value: Iron restriction post 60 minutes


title: H9-0h-1

value: doxorubicin for 0 hour


title: K-10 , iron deplete, 5 minutes, replicate 1

value: Iron restriction post 5 minutes


title: Donor.D2172_DARIC33_CD4_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
B5

value: CD4+ T cells

value: 1nM rapamycin


title: HK1_sgFLI1-2

first: wuguo

last: deng

address: 651 Dongfengdongroad, Guangzhou, Guangdog

institute: Sun yat-sen university

data_processing:
RNA-Seq data underwent adaptor trimming, and data quality assessment was performed using fastp software (v 0.23.2) prior to any data filtering steps.
The reads were aligned to the human reference genome (GRCh38.p12 assembly) using HISAT2 software (v 2.0.4).
The aligned reads were then assembled into transcripts or genes using StringTie software (v 1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf).
For quantification purposes, the relative abundance of the transcripts/genes was determined using a normalized metric called FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: hg38
Supplementary files format and content: excel file includes raw counts for each Sample
Supplementary files format and content: excel file includes RPKM  values for each Sample

source_name: nasopharynx

extract_protocol:
RNA extraction was performed with the AllPrep RNA/DNA Mini Kit (Qiagen) according to manufacturer’s instructions.
The NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) was employed for generating sequencing libraries, following the manufacturer's guidelines.

value: nasopharynx

value: Nasopharyngeal carcinoma cells

value: FLI1 knockout


title: K-10 , iron replete, replicate 2

value: No iron restriction- control


title: K-10 , iron replete, replicate 1


title: DBA_Sham_c

value: synovial membrane

value: sham

value: regular diet


title: Donor.D732_DARIC33_CD8_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
C5

value: CD8+ T cells

value: Unstimulated


title: K-10 , iron deplete, 30 minutes, replicate 1

value: MAP K-10- Parent strain

value: Iron restriction post 30 minutes


title: HFDBA_CIA_a

value: collagen-induced-arthritis (CIA)

value: high-fat diets (HFD)


title: HK1_sgFLI1-1


title: Donor.D932_DARIC33_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_168h

description:
Two technical replicates of 150bp PE
A5

value: CD33+ MV4-11 AML target cells


title: HK1_WT

value: WT


title: Donor.D1173_Untransduced_CD4_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
F4

value: CD4+ T cells

value: Untransduced


title: DBA_Sham_a


title: HK1_Flag-FLI1_IFN-gamma, Input

data_processing:
Raw reads underwent a filtering process to obtain high-quality clean reads, which involved removing sequencing adapters, short reads (length <35 bp), and low-quality reads using Cutadapt v1.18.
The high read quality was further confirmed using FastQC. Next, the clean reads were aligned to the human genome (assembly GRCh38) utilizing the Bowtie2 v2.3.4.1 software.
Duplicate reads were subsequently eliminated using picard MarkDuplicates.
Peak detection was carried out using the MACS v2.1.2 peak finding algorithm, with a p-value cutoff set at 0.01 to identify statistically significant peaks.
Annotation of the identified peak sites to gene features was accomplished using the ChIPseeker R package.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes, followed by quenching with 125 mM glycine. The chromatin was subsequently  fragmented, lysed and sonicated.
The DNA libraries were amplified through 15 cycles of PCR and were then subjected to sequencing using the Illumina Hi-Seq platform with paired-end 2X150 as the sequencing mode.

value: nasopharynx

value: FLI1 overexpression

value: IFN-gamma


title: Donor.D2172_DARIC33_CD8_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
E4

value: media alone


title: DBA_CIA_c

value: synovial membrane


title: DBA_CIA_b


title: HK1_Flag-FLI1_Control, Input

value: Nasopharyngeal carcinoma cells

value: Control


title: HK1_Flag-FLI1_IFN-gamma, Flag


title: Donor.D932_Untransduced_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
C4

value: CD8+ T cells

value: 1nM rapamycin


title: DBA_CIA_a

value: regular diet


title: DBA_Sham_b

value: sham


title: Donor.D1173_DARIC33_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_168h

description:
Two technical replicates of 150bp PE
B4


title: Donor.D1173_Untransduced_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
A4


title: WT_biol_rep6

city: Xiamen

first: jiepeng

last: guan

address: Xiamen University

institute: Xiamen University

description:
WT_vs_KO_TPM
edgeR_WT_vs_KO

data_processing:
The reads obtained from the sequencing machines including adapters or low-quality bases were filtered by trim-galore (version 0.6.10).
The reads of ribosome RNA (rRNA) were removed by hisat2 (version 2.2.1).
The remaining paired-end clean reads were aligned to the plasmodium genome using hisat2 (version 2.2.1)
Read counts per transcript were obtained by using featureCounts (version 2.0.3)
TPM values for each gene in each samples were calculated by using the R package t-arae/ngscmdr (version 0.1.0.181203)
Read counts TMM normalization and differential gene analysis were performed by using edgeR (version 3.16)
Assembly: GCA_900002385
Supplementary files format and content: csv files include TPM normalized for each Sample
Supplementary files format and content: csv files include log2FoldChange, p-values, FDR and TMM normalized counts generated from edgeR for each Sample

molecule: polyA RNA

organism: Plasmodium yoelii

extract_protocol:
Total RNA from 2×107sex-sorted gametocytes was extracted using TRIzol.
RNA integrity was checked with the Agilent 2100 Bioanalyzer. mRNA was then enriched by Oligo(dT) beads. The enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase Ⅰ, RNase H, dNTP and buffer. The cDNA fragments were purified with the QIAQuick PCR Purification Kit, end-repaired, A tailed, and ligated to Illumina sequencing adapters. The ligation products were size-selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).

value: Male gametocyte


title: HK1_Flag-FLI1_Control, Flag


title: HK1_sgFLI1_Ifn-gamma

data_processing:
Raw sequencing reads underwent a series of preprocessing steps to obtain high-quality clean reads. This involved removing sequencing adapters, short reads with a length less than 35 bp, and low-quality reads using Trimmomatic v0.3.
FastQC was employed to ensure the quality of the resulting reads. The clean reads were then aligned to the human genome (assembly GRCh38) using the Bowtie2 v2.3.4.1 software. Alignments with low mapping quality scores (MAPQ < 30). were filtered out using samtools.
To further improve data quality, duplicate reads were removed using the picard MarkDuplicates (http://broadinstitute.github.io/picard). For peak detection, the MACS v2.1.2 peak finding algorithm was utilized with a q-value cutoff of 0.05 to identify significant peaks.
To evaluate the reproducibility of the high-throughput experiments, the irreproducible discovery rate (IDR v2.0.2) analysis was performed, and only reproducible peaks with an IDR value of 0.05 or less were retained. Next, the peak sites were annotated to gene features using the ChIPseeker R package.
To detect potential motifs within the identified peaks, the MEME suite (http://meme-suite.org/) was employed. Lastly, differential peaks between two comparison groups were identified using The DiffBind with a q-value cutoff of 0.05.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
Cell lysis occurred using a cold lysis buffer comprising 10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, and 0.1% IGEPAL CA-630. Nuclei were promptly spun at 500 × g for 10 minutes at 4℃, with subsequent discarding of the supernatant.
After purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM custom Nextera PCR primers. The PCR conditions involved an initial step at 72°C for 5 minutes, followed by denaturation at 98°C for 30 seconds, and subsequent thermocycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. A final extension step was performed at 72℃ for 5 minutes. The libraries were then purified using a Qiagen PCR cleanup kit, resulting in the final library.

value: FLI1 knockout


title: Levels of miRNAs in the plasma exosomes of mice bearing A549Ago2-KO/HA-Ago4Δ (Dm) tumors

type: RNA

city: Miaoli County

first: LU

middle: LI

last: YU

address: 35, Keyan Road, Zhunan Town,

country: Taiwan

institute: ational Health Research Institutes

description: miRNA expression data from mice plasma  exosomes

hyb_protocol: 21.5 μLof Biotin-labeled sample were hybridized for 16 hr at 48℃ on miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G.

data_processing: Affymetrix GeneChip Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then Affymetrix Expression Console 1.3.1. for normalization; Partek Genomics Suite software for statistical analysis

label: biotin

organism: Mus

source_name: miRNA from DM mice plasma exosome

label_protocol: Biotinylated miRNA were prepared using FlashTag Biotin HSR RNA Labeling Kit.

growth_protocol: Animals complied with protocols approved by the NHRI Committee on Animal Care

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

treatment_protocol: A549Ago2-KO/Ago2Wt and A549Ago2-KO/Ago2Δ cells were subcutaneously implanted in SCID mice. All mice that were injected with either 1 × 106 A549Ago2-KO/Ago2Wt. Plasma exosomes were collected  and total RNA (included miRNA) werw extracted by Trizol reagent

value: plasma exosome

value: A549Ago2-KO/HA-Ago2Δ (Dm) tumors


title: Levels of miRNAs in the plasma exosomes of mice bearing A549Ago2-KO/HA-Ago2Δ (Dm) tumors


title: HK1-WT_IFN-gamma

value: WT


title: Levels of miRNAs in the plasma exosomes of mice bearing A549Ago2-KO/HA-Ago3Δ (Dm) tumors


title: WT_biol_rep5

description:
WT_vs_KO_TPM
edgeR_WT_vs_KO


title: Donor.D1173_DARIC33_CD4_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
F3

data_processing:
Reads were filtered for quality and aligned to the Genome Resource Consortium hg38 human genome reference using STAR (2.6.1d).
Gene expression was quantified as transcripts per million (TPM) using RSEM (1.3.1).
Assembly: hg38
Supplementary files format and content: comma-delimited text file contains RSEM TPMs for each sample.
Supplementary files format and content: comma-delimited text file contains RSEM expected counts for each sample.

extract_protocol:
Total RNA was isolated using the Qiagen 96-well RNeasy Prep Kit.
Libraries were generated using KAPA 148 Hyperprep Kit with RiboErase and KAPA Unique Dual-Indexed Adapter Kit (Roche).
The sequencing strategy was two technical replicates of 150bp paired-end reads.  Samples were sequenced on a NextSeq500 instrument.

value: CD4+ T cells

value: Unstimulated


title: Levels of miRNAs in the plasma exosomes of mice bearing A549Ago2-KO/HA-Ago4Wt tumors

source_name: miRNA from WT mice plasma exosome

value: A549Ago2-KO/HA-Ago2Wt tumors


title: WT_biol_rep4

description:
WT_vs_KO_TPM
edgeR_WT_vs_KO


title: Donor.D732_Untransduced_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
E3

value: Untransduced

value: CD33+ MV4-11 AML target cells


title: Levels of miRNAs in the plasma exosomes of mice bearing A549Ago2-KO/HA-Ago5Wt tumors


title: Donor.D2172_DARIC33_CD4_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
D4

value: media alone


title: HK1_sgFLI1_Control

value: nasopharynx

value: Nasopharyngeal carcinoma cells


title: Levels of miRNAs in the plasma exosomes of mice bearing A549Ago2-KO/HA-Ago2Wt tumors


title: 3_2(P2)  treated A549

city: Miaoli

first: meng chieh

last: lin

address: 35 Keyan Road

institute: National Health Research Institutes

description: 3_2(P2S) [3_2.rma-dabg.chp Signal]

hyb_protocol: 21.5 μLof Biotin-labeled sample were hybridized for 16 hr at 48℃ on miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: miRNA from P2 peptide treated A549 cells

growth_protocol: A549 were propagated in DMEM medium according to standard protocols.

treatment_protocol: A549 cells were treated with blocking peptides-P2 and scramble-P2 (10μM daily) for 2day, then harvested and extracted total RNA for miRNA microarray 4.0 array.

value: Human Lung cancer  cell line

value: P2-peptide treated


title: HK1-WT_Control

value: Control


title: Donor.D932_DARIC33_CD4_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
D3


title: 3_1(P2S)  treated A549

description: 3_1(P2S) [3_1.rma-dabg.chp Signal]

source_name: miRNA from P2S peptide treated A549 cells

value: P2S-peptide treated


title: Py17XNL_MG_Rep3

value: Male gametocyte


title: 2_2(P2S)  treated A549

description: 2_2(P2) [2_2.rma-dabg.chp Signal]


title: Py17XNL_MG_Rep2


title: HONE-1 cells, siKLF5 2#

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nasopharyngeal carcinoma cells

value: KLF5 knockdown


title: Py17XNL_MG_Rep1


title: Donor.D932_Untransduced_CD8_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
B3

value: CD8+ T cells

value: 1nM rapamycin


title: HONE-1 cells, siKLF5 1#


title: 2_1(P2)  treated A549

description: 2_1(P2S) [2_1.rma-dabg.chp Signal]


title: Female biol rep3

data_processing:
The reads obtained from the sequencing machines including adapters or low-quality bases were filtered by fastp (version 0.18.0).
The reads of ribosome RNA (rRNA) were removed by the short reads alignment tool Bowtie2 (version 2.2.8).
The remaining paired-end clean reads were aligned to the plasmodium genome using HISAT2.
Read counts per transcript were obtained by the HTSeq-Counts package with default parameters
Assembly: The mapped reads were assembled with StringTie v1.3.1
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: yoelii 17XNL

value: yoelii 17XNL

value: Female gametocyte

value: WT


title: HONE-1 cells, negative control


title: E0771, Malt1_L88D, Rep3

city: Beijing

first: Hanqiu

last: Zheng

address: Haidian District

institute: Tsinghua university

data_processing:
The adaptors of paired-end reads were trimmed and quality control checks were carried out using trim-galore (v.0.6.0). Reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using STAR (v.2.7.3a). featureCounts (v.1.6.3) counted reads stored in BAM format to exon sites of genes included in GTF files from GENCODE.
Assembly: GRCm38.p6

extract_protocol:
Total RNA was isolated from cells using RNAiso Plus Regent (Takara, Cat# 9108) following the manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat# E7765) was used to generate sequencing libraires from 1 μg of total RNA. All library preparations were conducted according to the manufacturer’s instructions. Paired-end 150bp sequencing was performed using an Illumina NovaSeq platform.

value: cancer cell


title: Donor.D2172_DARIC33_CD8_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
A3

value: Unstimulated


title: Donor liver biopsy-32

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
Bulk RNA-seq from liver tissue
HL32_AHII090

data_processing:
The nf-core RNA-seq pipeline (version 3.7; doi: 10.5281/zenodo.1400710) within the Nextflow framework (version 22.04.0)  was used to perform fastq preprocessing, quality assessment, transcriptome alignment, and transcript quantification (Ewels et al., 2020).
The STAR aligner was employed for transcriptome alignment (Dobin et al., 2013), while salmon was used for transcript quantification (Patro et al., 2017).
Assembly: GRCh38
Supplementary files format and content: Matrix table with  gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNA was extracted from the flash-frozen liver tissue samples using the miRNeasy Mini Kit (217004; Qiagen, Hilden, Germany) and stored at -80°C.
The libraries were constructed using Illumina Stranded Total RNA Prep with Ribo-Zero (20040525; Illumina, California, United States)
RNAseq was performed using Illumina NovaSeq 6000 (Illumina). Sequencing was paired-end (2x100 bp) at a read depth of 50 million reads per sample. Fastq generation was performed upon run completion using the Illumina basespace cloud.

value: liver

tag: Sex

value: Male

tag: race

value: African-American

tag: transplant-selection

value: Rejected


title: E0771, Malt1_L88D, Rep2

tag: cell line

tag: cell type


title: Donor liver biopsy-31

description:
Bulk RNA-seq from liver tissue
HL31_AHKU193

tag: tissue

value: Caucasian


title: Donor.D2172_Untransduced_CD8_media alone_Unstimulated_24h

first: Daniel

last: Zak

address: 188 East Blaine Street, Suite 300

institute: Regeneron

description:
Two technical replicates of 150bp PE
C3

value: Untransduced

tag: treatment

value: media alone


title: Female biol rep1

tag: genotype


title: Donor.D1173_DARIC33_CD8_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
E2

tag: transgene


title: 1_1(P2S) treated A549

description: 1_1(P2S) [1_1.rma-dabg.chp Signal]

value: Human Lung cancer  cell line

value: P2S-peptide treated


title: 1_2(P2)  treated A549

description: 1_2(P2) [1_2.rma-dabg.chp Signal]

value: P2-peptide treated


title: Male biol rep3

value: Male gametocyte


title: E0771, Malt1_L88D, Rep1


title: Female biol rep2


title: E0771, Malt1_V87R, Rep3


title: Male biol rep2


title: Donor liver biopsy-29

description:
Bulk RNA-seq from liver tissue
HL29_AIWL117

value: Female

value: Accepted


title: Donor.D2172_Untransduced_CD4_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
D2

source_name: CD4+ T cells

value: CD4+ T cells

tag: donor


title: Donor liver biopsy-30

description:
Bulk RNA-seq from liver tissue
HL30_AHJB400


title: Donor.D2172_DARIC33_CD4_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
C2

tag: stimulation


title: E0771, Malt1_V87R, Rep2


title: Male biol rep1

value: yoelii 17XNL

value: WT


title: E0771, Malt1_V87R, Rep1

value: cancer cell


title: Donor liver biopsy-28

description:
Bulk RNA-seq from liver tissue
HL28_AJCT312

value: liver


title: Donor.D732_DARIC33_CD4_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
B2

value: 1nM rapamycin

value: Unstimulated

tag: time


title: Donor liver biopsy-27

description:
Bulk RNA-seq from liver tissue
HL27_AJCN178

value: Male


title: Donor.D2172_Untransduced_CD4_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
F2


title: Donor liver biopsy-26

description:
Bulk RNA-seq from liver tissue
HL26_AIGS266

value: Caucasian


title: E0771, Malt1_PD, Rep3


title: Donor.D932_DARIC33_CD4_1nM rapamycin_Unstimulated_24h

description:
Two technical replicates of 150bp PE
F1


title: E0771, Malt1_PD, Rep2


title: Donor liver biopsy-25

description:
Bulk RNA-seq from liver tissue
HL25_AIDY465


title: Donor liver biopsy-24

description:
Bulk RNA-seq from liver tissue
HL24_AIBQ043

value: African-American


title: Donor.D732_Untransduced_CD4_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
E1

value: Untransduced

value: media alone


title: Donor.D1173_Untransduced_CD8_media alone_Unstimulated_24h

description:
Two technical replicates of 150bp PE
D1

source_name: CD8+ T cells

value: CD8+ T cells


title: E0771, Malt1_WT, Rep3


title: E0771, Malt1_PD, Rep1


title: Donor liver biopsy-23

description:
Bulk RNA-seq from liver tissue
HL23_AHGO418

value: Rejected


title: E0771, Malt1_WT, Rep1


title: Donor.D932_Untransduced_CD4_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
A1

value: CD33+ MV4-11 AML target cells


title: Donor.D2172_DARIC33_CD8_1nM rapamycin_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
C1


title: SACC-LM

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: salivary adenoid cystic carcinoma cell line SACC-LM

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: SACC-LM

value: salivary adenoid cystic carcinoma cell

tag: phenotype

value: high capacity for lung metastasis


title: Donor.D932_Untransduced_CD4_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
B1

value: CD4+ T cells


title: Donor.D732_Untransduced_CD8_media alone_CD33+ MV4-11 AML target cells_24h

description:
Two technical replicates of 150bp PE
A2


title: OE-2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and 1ow quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow: $$FPKM = {cDNA Fragments lover (Mapped Fragments (Mi11ions）* TranscriptLength (kb)}}$$
Assembly: GRCh38
Supplementary files format and content: list file includes FPKM values for each Sample

value: salivary adenoid cystic carcinoma cells

value: circMYBL2 overexpression


title: SACC-83

source_name: salivary adenoid cystic carcinoma cell line SACC-83

value: low capacity for lung metastasis


title: Pat80.BL-1

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.4 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.3 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Contrasts were created with DESeq2 based on the raw count matrix.
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized gene counts.

source_name: Right ventricular myocardial free wall biopsy

extract_protocol:
RNA isolation was performed with Qiagen miRNeasy micro Kit and Biozym bead bug 3 Homogenizer
100ng-1µg total RNA was used for Hi-Mammalian whole transcriptome preparation (Takara Bio). Sequencing was performed on Nextseq500 with 1x72bp single-end setup.

tag: disease state

value: CTEPH

tag: esc risk group

value: Severe

tag: individual

value: prePEA


title: E0771, Vector control, Rep2

value: cancer cell

value: Vector control


title: Donor liver biopsy-20

description:
Bulk RNA-seq from liver tissue
HL20_AHGI142

value: liver

value: Female

value: Caucasian


title: E0771, Vector control, Rep3


title: Donor liver biopsy-19

description:
Bulk RNA-seq from liver tissue
HL19_AHGW406

value: Rejected


title: Pat51.BL-1

value: Right ventricular myocardial free wall biopsy

value: Moderate


title: E0771, Vector control, Rep1


title: E0771, Malt1_WT, Rep2


title: Donor liver biopsy-22

description:
Bulk RNA-seq from liver tissue
HL22_AHG2102

value: Male


title: Donor liver biopsy-18

description:
Bulk RNA-seq from liver tissue
HL18_AHJQ339

value: Hispanic


title: Pat11.BL-1


title: E0771 Malt1_PD_Rep2 after T cell killing

data_processing: The adaptors of paired-end reads were trimmed and quality control checks were carried out using trim-galore (v.0.6.0). Reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using STAR (v.2.7.3a). featureCounts (v.1.6.3) counted reads stored in BAM format to exon sites of genes included in GTF files from GENCODE.

value: After T cell coculture


title: Donor liver biopsy-21

description:
Bulk RNA-seq from liver tissue
HL21_AIAC389


title: Donor liver biopsy-17

description:
Bulk RNA-seq from liver tissue
HL17_AIAJ296


title: Pat45.BL-1


title: Donor liver biopsy-16

description:
Bulk RNA-seq from liver tissue
HL16_AHHH143


title: SMG-9

source_name: SMG tissue-9

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: submandibular gland


title: Pat50.BL-1


title: SMG-7

source_name: SMG tissue-7


title: SMG-10

source_name: SMG tissue-10


title: SMG-5

source_name: SMG tissue-5


title: SMG-8

source_name: SMG tissue-8


title: SMG-4

source_name: SMG tissue-4


title: SMG-6

source_name: SMG tissue-6


title: SMG-2

source_name: SMG tissue-2


title: Pat3.BL-1


title: E0771 Malt1_WT_Rep2 after T cell killing


title: E0771 Malt1_WT_Rep1 after T cell killing


title: E0771 Vector control Rep2 after T cell killing


title: Donor liver biopsy-14

description:
Bulk RNA-seq from liver tissue
HL14_AHCE041


title: Quadriceps muscle, Non_transgenic control_1

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Assembly: mm10
Supplementary files format and content: Excel file represents raw counts with genes in rows and samples in columns

source_name: Quadriceps muscle

value: skeletal muscle

tag: strain

value: FVB/N

value: control


title: Donor liver biopsy-13

description:
Bulk RNA-seq from liver tissue
HL13_AHL5250

tag: Sex


title: Donor liver biopsy-12

description:
Bulk RNA-seq from liver tissue
HL12_AHIR183

tag: race


title: Donor liver biopsy-15

description:
Bulk RNA-seq from liver tissue
HL15_AHKN132

tag: transplant-selection


title: Pat59.BL-1

value: CTEPH

value: Severe


title: E0771 Malt1_PD_Rep1 after T cell killing

tag: cell line

value: cancer cell


title: Pat14.BL-1

value: prePEA


title: CD45+ cells of paracaspase-deficient Malt1 overexpression tumor

data_processing:
FASTQ reads of 10× scRNA sequencing data were processed with GRCh38 reference genome using Cell Ranger (version 3.1, 10× Genomics). Downstream analyses of scRNA-seq data were performed in Seurat package version 3.2.0.(https://www.cell.com/cell/fulltext/S0092-8674(19)30559-8). Low quality cells were excluded from downstream analyses based on %mitochondrial reads <10, features per cell >500. All functions were run with default parameters. Identification of cell types is determined by the expression of the immune cell marker gene.
Assembly: hg38
Supplementary files format and content: single-cell RNA-seq expression counts files and matrix files

source_name: tumor

extract_protocol:
Single cell suspensions isolated from tumors developed from E0771-Vector control tumor tissue, E0771 Malt1-WT overexpression tumor tissue and E0771 paracaspase-deficient Malt1 (Malt1-PD) overexpression tumor tissue. About 10000 CD45+ live cells were sorted from tumors of each strain by BD FACS Aria ii. Reverse transcription, cDNA amplification and library preparation were performed using the Chromium Single Cell V(D)J Reagent Kits (10x Genomics, includes Cat# PN-1000006, Cat# PN-1000020, Cat# PN-1000009, and Cat # PN-120262) according to manufacturer’s protocol. Pair-end 150 bp sequencing was performed on Illumina HiSeq X Ten platform by Novogene Co.,Ltd. Single cell sequence data was pre-processed with Cell Ranger 3.0.2 (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, CD45+ cells in each group were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: tumor

tag: cell type

value: immune cell


title: E0771 Vector control Rep1 after T cell killing


title: Donor liver biopsy-11

description:
Bulk RNA-seq from liver tissue
HL11_AHKC275

tag: tissue

value: liver

value: Female

value: Caucasian


title: Patient_3

city: Pamplona

first: Guillermo

last: Serrano

state: Navarra

address: Av. de Pío XII, 55

country: Spain

institute: CIMA - Universidad de Navarra

description: Diagnosed with 90% del(5q)

data_processing:
Demultiplexing, alignment to the hg38 genome and quantification was carried out with Cellranger (v3.1)
Posterior analysis (quality control, clustering, integration and differential expression) was performed with Seurat v4.2
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files, containing the name of genes, barcodes and raw counts.
Supplementary files format and content: Tab-separated values files, containing the annotation of the cells having passed the QC and the presence or absence of the deletion of the 5q region.

source_name: Bone Marrow

extract_protocol:
Cells were sorted by FACS based on the presence of CD34 from bone marrow aspirates.
Single cell 3’ RNA sequencing libraries were prepared using the chromiun controller from 10X Genomics. NEXTGEM Single Cell 3' Reagent Kits v3 and v3.1  were used

value: Bone Marrow

value: Tissue

tag: treatment

value: Diagnosed with 90% del(5q)


title: CD45+ cells of wildtype Malt1 overexpression tumor

value: Wildtype Malt1 overexpression


title: Donor liver biopsy-10

description:
Bulk RNA-seq from liver tissue
HL10_AHIE299

source_name: liver

value: Male

value: Rejected


title: CD45+ cells of Vector control overexpression tumor

value: vector control overexpression


title: Patient_2

description: Diagnosed with 75% del(5q)

value: Diagnosed with 75% del(5q)


title: Donor liver biopsy-9

description:
Bulk RNA-seq from liver tissue
HL09_AHKL087


title: Donor liver biopsy-8

description:
Bulk RNA-seq from liver tissue
HL08_AHH5160


title: Patient_1

description: Diagnosed with 43% del(5q)

value: Diagnosed with 43% del(5q)


title: Human stem cell-derived brain-like ECs, cARLA treated, rep4

city: Frankfurt am Main

first: Ricardo

middle: Mamede

last: Figueiredo

address: Altenhöferallee 3

institute: GenXPro GmbH

data_processing:
Illumina bcl2fastq2 v2.20 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
PCR duplicates were cleaned using TrueQuant technology (UMI) and in-house GenXPro GmbH script.
Reads were aligned to the human reference genome (hg38) using the bowtie2 2.3.4.1 mapping tool.
Gene count data was normalized to account for differences in sequencing depth. Testing for differential gene expression was performed in the statistical programming platform R using the DeSeq2 R/Bioconductor package.
Assembly: Genome Reference Consortium Human Build 38 (hg38)
Supplementary files format and content: Comma-delimited text file include raw counts for each sample

growth_protocol: Human stem cell-derived brain-like endothelial cells (in co-culture with primary bovine brain pericytes) were grown on Transwell inserts (Corning, cat# 3401) for 6 days. Cells were kept in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
Pericytes were removed and endothelial cells were lysed directly with Buffer RLT Plus (Qiagen, cat# 1053393) on the inserts. For 1 sample in further analyses, cell lysates from 2 inserts were pooled. RNA was isolated using RNeasy Plus Micro Kit (Qiagen, cat# 74034) containing an integrated gDNA eliminator spin column according to the manufacturer’s protocol.
For library preparation, samples with 1 µg of purified RNA were used. A total of 8 libraries (4 control and 4 cARLA) were constructed using the Rapid MACE-Seq kit (GenXPro GmbH, Frankfurt, Germany) according to the manufacturer’s protocol. Fragmented RNA was reverse transcribed into cDNA, using barcoded oligo(dT) primers containing TrueQuant unique molecular identifiers, followed by template switching. Library amplification was done using polymerase chain reaction (PCR), purified by solid phase reversible immobilization beads (Agencourt AMPure XP, Beckman Coulter, cat# A63882).

treatment_protocol: cARLA treatment consisted of 250 µM cAMP (cPT-cAMP; Sigma-Aldrich, cat# C3912) + 17.5 µM Ro (Sigma-Aldrich, cat# 557502) + 3 mM LiCl (LiCl; Sigma-Aldrich, cat# L9650) + 3 µM A83-01 (PeproTech, cat# 9094360). For the last 48 hours, endothelial cells were treated with cARLA or control medium containing the amount of solvents (Milli-Q water 100× and DMSO 1000× dilution) corresponding to cARLA.

value: Endothelial cell

value: cARLA (250 uM cAMP + 17.5 uM Ro + 3 mM LiCl + 3 uM A83-01)


title: Donor liver biopsy-7

description:
Bulk RNA-seq from liver tissue
HL07_AHLJ351


title: Human stem cell-derived brain-like ECs, cARLA treated, rep3

source_name: Human stem cell-derived brain-like endothelial cells


title: SMG-3

source_name: SMG tissue-3

value: submandibular gland


title: SMG-1

source_name: SMG tissue-1


title: Donor liver biopsy-6

description:
Bulk RNA-seq from liver tissue
HL06_AHK2146

value: Hispanic


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2Δ(Dm) cells, 1

first: YI-JU

last: CHEN

address: Room R1-3121, 35 keyan Road, Zhunan Town

description: miRNA expression data from A549 cells

source_name: miRNA from A549 Ago2-KO/HA-Ago2Δ(Dm) cells

growth_protocol: A549 Ago2-KO/HA-Ago2Wt, Ago2-KO/HA-Ago2KA, and Ago2-KO/HA-Ago2Δ (Dm)  cells were seeded into 15-cm dishes (2 × 106 cells per dish) and  incubated for 3 days.

treatment_protocol: A549 Ago2-KO/HA-Ago2Wt, Ago2-KO/HA-Ago2KA, and Ago2-KO/HA-Ago2Δ (Dm)  cells were collected  and total RNA (included miRNA) werw extracted by Trizol reagent.

tag: genotype

value: Ago2-KO, and OE HA-Ago2Dm cells


title: SACC-10

source_name: SACC tissue-10

value: salivary adenoid cystic carcinoma


title: Human stem cell-derived brain-like ECs, cARLA treated, rep2

value: Human stem cell-derived brain-like endothelial cells


title: SACC-8

source_name: SACC tissue-8


title: SACC-9

source_name: SACC tissue-9


title: KORbpm1 biol rep3

data_processing:
The reads obtained from the sequencing machines including adapters or low-quality bases were filtered by fastp (version 0.18.0).
The reads of ribosome RNA (rRNA) were removed by the short reads alignment tool Bowtie2 (version 2.2.8).
The remaining paired-end clean reads were aligned to the Plasmodium genome using HISAT2.
Read counts per transcript were obtained by the HTSeq-Counts package with default parameters.
The mapped reads were assembled with StringTie v1.3.1.
Assembly: not provided
Supplementary files format and content: Rbpm1_knockout.txt: Tab-delimited text file includes counts and FPKM values for each sample.

organism: Plasmodium yoelii yoelii 17XNL

source_name: Male gametocyte

extract_protocol:
Total RNA from 2×10^7sex-sorted gametocytes was extracted using TRIzol.
RNA integrity was checked with the Agilent 2100 Bioanalyzer. mRNA was then enriched by Oligo(dT) beads. The enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. The cDNA fragments were purified with the QIAQuick PCR Purification Kit, end-repaired, A tailed, and ligated to Illumina sequencing adapters. The ligation products were size-selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).

value: Male gametocyte

value: Rbpm1 knockout


title: SACC-6

source_name: SACC tissue-6


title: SACC-4

source_name: SACC tissue-4


title: Donor liver biopsy-5

description:
Bulk RNA-seq from liver tissue
HL05_AHLH202

value: liver

value: Female

value: Caucasian


title: SACC-1

source_name: SACC tissue-1


title: Pat1.BL-1

source_name: Right ventricular myocardial free wall biopsy

value: CTEPH

value: Severe

value: Male

value: prePEA


title: SACC-3

source_name: SACC tissue-3


title: SACC-7

source_name: SACC tissue-7


title: SACC-5

source_name: SACC tissue-5


title: Human stem cell-derived brain-like ECs, cARLA treated, rep1


title: KORbpm1 biol rep2


title: Donor liver biopsy-4

description:
Bulk RNA-seq from liver tissue
HL04_AHHQ205

value: Accepted


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2KA cells, 3

description: miRNA expression data from A549 cells

source_name: miRNA from A549 Ago2-KO/HA-Ago2KA cells

value: Ago2-KO, and OE HA-Ago2KA cells


title: Human stem cell-derived brain-like ECs, untreated, rep4

value: Endothelial cell

value: Control


title: Donor liver biopsy-3

description:
Bulk RNA-seq from liver tissue
HL03_AHHC458

source_name: liver

value: Hispanic


title: Human stem cell-derived brain-like ECs, untreated, rep3

source_name: Human stem cell-derived brain-like endothelial cells


title: WT biol rep3

value: WT


title: KORbpm1 biol rep1


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2Δ(Dm) cells, 3

description: miRNA expression data from A549 cells

value: Ago2-KO, and OE HA-Ago2Dm cells


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2Δ(Dm) cells, 2

description: miRNA expression data from A549 cells


title: Donor liver biopsy-2

description:
Bulk RNA-seq from liver tissue
HL02_AIBF419


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2KA cells, 2

description: miRNA expression data from A549 cells


title: WT biol rep2


title: Human stem cell-derived brain-like ECs, untreated, rep2

value: Human stem cell-derived brain-like endothelial cells


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2Wt cells, 3

description: miRNA expression data from A549 cells

source_name: miRNA from A549 Ago2-KO/HA-Ago2Wt cells

value: Ago2-KO, and OE HA-Ago2Wt cells


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2KA cells, 1

description: miRNA expression data from A549 cells


title: Donor liver biopsy-1

description:
Bulk RNA-seq from liver tissue
HL01_AHLX028


title: SACC-2

source_name: SACC tissue-2

value: salivary adenoid cystic carcinoma


title: WT biol rep1

value: Male gametocyte


title: RNA-seq in E18.5 wild type male urogenital sinus replicate 1

status: Public on Apr 17 2024

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

data_processing:
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw RNA-seq reads were processed with CutAdapt version 4.1 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 30 -m 15) to remove TruSeq adapters and bad quality bases.
Filtered reads were mapped on the mouse genome mm39 with STAR version 2.7.10a with ENCODE parameters with a custom gtf file based on Ensembl version 108 (10.5281/ZENODO.7510796). This custom gtf file was obtained by removing readthrough transcripts and all noncoding transcripts from a protein-coding gene.
FPKM values were evaluated by Cufflinks version 2.2.1 with options --max-bundle-length 10000000 --multiread-correct --library-type “fr-firststrand” -b mm10.fa --no-effective-length-correction -M MTmouse.gtf -G
Uniquely mapped reads were filtered using the "NH:i:1" tag. Coverage (strand specific or not) were computed with bedtools version 2.30.0 using the ‘-scale’ argument to normalize to the million uniquely mapped reads.
Assembly: mm39
Supplementary files format and content: _Uniq_norm.bw: Normalized coverage strand unspecific
Supplementary files format and content: _Uniq_fwd_norm.bw: Normalized coverage on the forward strand
Supplementary files format and content: _Uniq_rev_norm.bw: Normalized coverage on the reverse strand
Supplementary files format and content: AllCufflinks_Simplified.txt.gz: All FPKM values into a single table (multiple lines for the same gene id were summed)

source_name: urogenital sinus

extract_protocol:
E18.5 male and female UGS were collected with a dissection separating the bladder from the urogenital sinus but including the proximal urethra (and vagina in females). Tissues were stored in RNALater (ThermFisher AM7020) and processed in parallel with Qiagen RNeasy extraction kits (Qiagen 74034). RNA quality was assessed on an Agilent Bioanalyzer 2100, with RIN scores > 9.5.
RNA sequencing libraries were prepared at the University of Geneva genomics platform using Illumina TruSeq stranded total RNA with Ribo-Zero TM Gold Ribo-deleted RNA kits to produce strand-specific single-end reads.

value: urogenital sinus

value: male

tag: Stage

value: wild type


title: RNA-seq in E18.5 wild type female urogenital sinus replicate 2

value: female


title: RNA-seq in E18.5 wild type female urogenital sinus replicate 3


title: RNA-seq in E18.5 wild type male urogenital sinus replicate 2


title: RNA-seq in E18.5 wild type male urogenital sinus replicate 3


title: RNA-seq in E18.5 mutant male urogenital sinus replicate 1


title: RNA-seq in E18.5 wild type female urogenital sinus replicate 1


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2Wt cells, 2

description: miRNA expression data from A549 cells


title: RNA-seq in E18.5 mutant male urogenital sinus replicate 2


title: RNA-seq in E18.5 mutant female urogenital sinus replicate 2


title: RNA-seq in E18.5 mutant male urogenital sinus replicate 3


title: Levels of miRNAs in the A549 Ago2-KO/HA-Ago2Wt cells, 1

description: miRNA expression data from A549 cells


title: WT H3K56ac ChIP rep3

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

description: synchronized to G2 ending, nascent DNA on S10 min

data_processing:
mapped to pombe reference genome by Bowtie2
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Origins were called by MACS2 from BrdU-IP
Assembly: pombe, ASM294v2
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position
Library strategy: eSPAN-seq

organism: Schizosaccharomyces pombe

growth_protocol: Strains containing the cdc25-22 temperature-sensitive mutant were first grown at permissive temperature (25°C) until the early-mid log phase (OD 0.2~0.4). Cultures were then incubated at 36°C for 4 hours to arrest cells at the G2 phase of the cell cycle. Cells were then shifted to 25°C to allow them to enter the S phase synchronously.

extract_protocol:
Cells were crosslinked at 60 minutes after temperature shift with the addition of 1% formaldehyde and incubated for 20 minutes with shaking at 25°C. Immunoprecipitation was performed as described in ChIP. Crosslinking was reversed by Chelex-100. Briefly, total and ChIP DNA were incubated at 100°C for 5 minutes and then immediately cooled on ice for 5 minutes. DNA was diluted ten times with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v)), and incubated with BrdU antibody (BD Bioscience 555627) for two hours at 4°C. Next, Sepharose Protein G beads (Cytiva 17-0618-01) were added and incubated for an additional one hour at 4°C. The beads were then washed three times with BrdU IP buffer and once with TE. Finally, DNA was eluted with TES and purified with the QIAGEN MinElute PCR Purification kit (Qiagen 28004).
AccelNGS 1S Plus DNA library kit (Swift Bioscience, 10096).

treatment_protocol: BrdU was added to a final concentration of 650 μM at 25minutes after the temperature shift.

tag: sample type

value: fission yeast

value: H3K56ac ChIP


title: WT H3K56ac eSPAN rep3

value: H3K56ac eSPAN


title: RNA-seq in E18.5 mutant female urogenital sinus replicate 1


title: WT BrdU rep7

value: BrdU


title: Ileum_Ms18_ABX

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The paired-end reads were demultiplexed using Casava v1.8.2 and cutadapt (v1.9) was used for read trimming.
The trimmed reads were subsequently mapped to the mouse genome (mm10) using HISAT2.
FeatureCounts was used for read counting after which differential gene expression analysis was perforemd using Voom-LIMMA packages
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Ileum

growth_protocol: Mice were maintained under conventional SPF conditions

extract_protocol:
RNA was purified using Nucleospin RNAXS column kit as per manufacturer’s instructions without adding a carrier RNA
Library was prepared using SMARTer Stranded Total RNA-Seq Pico-Input Mammalian kit v.3

treatment_protocol: Mice were given free access to drinking water or driking water supplemented with antibiotics

value: Ileum

value: wild-type

value: ABX


title: Ileum_Ms19_ABX


title: WT Input rep7

value: WT

value: Input


title: Ileum_Ms17_Water

value: Water


title: Ileum_Ms20_ABX


title: mcm22A_dpb4D_H3K9me3_eSPAN rep2

description: add tetO_MT

data_processing:
mapped to pombe reference genome by Bowtie2
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Origins were called by MACS2 from BrdU-IP
Assembly: pombe, ASM294v2
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position

source_name: fission yeast

extract_protocol:
Cells were crosslinked at 60 minutes after temperature shift with the addition of 1% formaldehyde and incubated for 20 minutes with shaking at 25°C. Immunoprecipitation was performed as described in ChIP. Crosslinking was reversed by Chelex-100. Briefly, total and ChIP DNA were incubated at 100°C for 5 minutes and then immediately cooled on ice for 5 minutes. DNA was diluted ten times with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v)), and incubated with BrdU antibody (BD Bioscience 555627) for two hours at 4°C. Next, Sepharose Protein G beads (Cytiva 17-0618-01) were added and incubated for an additional one hour at 4°C. The beads were then washed three times with BrdU IP buffer and once with TE. Finally, DNA was eluted with TES and purified with the QIAGEN MinElute PCR Purification kit (Qiagen 28004).
AccelNGS 1S Plus DNA library kit (Swift Bioscience, 10096).
eSPAN-seq


title: Ileum_Ms16_Water


title: mcm22A_dpb4D_H3K9me3_ChIP rep2

description: add tetO_MT


title: Human stem cell-derived brain-like ECs, untreated, rep1

value: Human stem cell-derived brain-like endothelial cells

value: Endothelial cell

value: Control


title: Ileum_Ms15_Water


title: mcm22A_dpb4D_BrdU rep6

description: add tetO_MT


title: Spleen_Ms20_ABX

source_name: Spleen

value: Spleen


title: mcm22A_dpb4D_Input rep6

description: add tetO_MT


title: Spleen_Ms19_ABX


title: RNA-seq in E18.5 mutant female urogenital sinus replicate 3

value: urogenital sinus


title: Spleen_Ms16_Water


title: mcm22A_dpb4D_Input rep5

description: add tetO_MT


title: Spleen_Ms18_ABX


title: mcm22A_dpb4D_H3K9me3_ChIP rep1

description: add tetO_MT


title: mcm22A_dpb4D_H3K9me3_eSPAN rep1

description: add tetO_MT


title: Spleen_Ms15_Water


title: Spleen_Ms17_Water


title: dpb4D_H3K9me3_eSPAN rep2

description: add tetO_MT


title: dpb4D_BrdU rep6

description: add tetO_MT


title: dpb4D_Input rep6

description: add tetO_MT


title: Infected+IFN-γ

city: Philadelphia

first: Ryan

last: Pardy

address: 380 South University Ave

department: Pathobiology

institute: University of Pennsylvania

description:
maCp_IFNg_GKO
10x Chromium Single Cell 3’ Library v3.1 chemistry, NextSeq 2000 P3 Kit (100 cycles).

data_processing:
Cell Ranger v7.0.0 was used to process sequencing reads and build a reference genome for C. parvum Iowa II (VEuPathDB, release 46). Processed reads from each sample were aligned to this reference genome or to the Mus musculus genome (GRCm38) to generate filtered feature-barcode matrices, which are the features (tsv), barcodes (tsv), and matrix (mtx) files listed in this submission.
Seurat 3.1.4 was used for filtering, normalization, clustering, UMAP visualization, and marker identification between IEC clusters.
Monocle3 was used to produce pseudotime trajectories.
Single-sample gene set enrichment analysis was performed using escape.
Assembly: GRCm38 of the Mus musculus reference genome from the Genome Reference Consortium.
Assembly: Version 46 of the Cryptosporidium parvum Iowa II reference from VEuPathDB.
Supplementary files format and content: The filtered_feature_bc_matrix (Cell Ranger 3.1.0 output) consists of features (tsv), barcodes (tsv), and matrix (mtx) files. The features (tsv) files are the same for all samples, and differ only whether they are for the mouse or C. parvum genome. The RDS files contain the Seurat objects for IEC clusters from each dataset (WT or IFNg_KO), with corresponding csv files containing the metadata information.

source_name: Murine epithelium from the ileum of the small intestine

extract_protocol:
Following isolation and dead cell removal, cells from mice were washed in 1X PBS (calcium and magnesium free) supplemented with 0.04% w/v BSA, centrifuged, and resuspended in 1X PBS (calcium and magnesium free) supplemented with 0.04% w/v BSA. Cells were then loaded onto a chromium chip for encapsulation via the 10x Genomics platform.
10x Chromium Single Cell 3’ Library v3.1 chemistry was used and manufacturer’s instructions were followed for cDNA amplification and library construction. For C57BL/6 samples, the NextSeq 500/550 High Output Kit v2.5 (75 cycles) was used to obtain paired-end reads from an Illumina NextSeq 500 sequencer. For IFNg KO samples, the NextSeq 2000 P3 Kit (100 cycles) was used to obtain paired-end reads from an Illumina NextSeq 2000.

treatment_protocol: C57BL/6 and IFN-gamma KO mice were infected with mouse-adapted C. parvum that has been engineered to express mCherry and nanoluciferase (see Gullicksrud et al. 2021). Two mice per group were infected with 50,000 oocysts and mice were sacrificed on days 4 and 10 (C57BL/6 mice) or 12 hours post-administration of PBS or IFNg (5dpi; IFNg KO mice). Epithelial cells were obtained from the small intestine and pooled within each group.

value: IFNg KO

tag: infection

value: Infected with 5x10e4 maCp oocysts

value: IFN-gamma

tag: cell preparation

value: single cell


title: dpb4D_H3K9me3_ChIP rep1

description: add tetO_MT

value: fission yeast


title: Uninf

description:
Uninf_GKO
10x Chromium Single Cell 3’ Library v3.1 chemistry, NextSeq 2000 P3 Kit (100 cycles).

value: Uninfected

value: PBS

value: Murine epithelium from the ileum of the small intestine


title: Infected

description:
maCp_GKO
10x Chromium Single Cell 3’ Library v3.1 chemistry, NextSeq 2000 P3 Kit (100 cycles).


title: dpb4D_H3K9me3_ChIP rep2

description: add tetO_MT


title: dpb4D_H3K9me3_eSPAN rep1

description: add tetO_MT


title: dpb4D_BrdU rep5

description: add tetO_MT

value: BrdU


title: VASAseq on Asynch. RPE1 CAF1 30hrs dTAG treated cells replicate 1

city: Utrecht

first: Francesca

last: Mattiroli

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
ATAC Libraries were sequenced 2x50 bp on Illumina NextSeq2000, scEdU-seq Libraries were sequenced 2x100 bp on Illumina NextSeq2000, VASA-seq libraries were sequenced 2x100bp on Illumina Nextseq2000, ChiC-seq libraries were sequenced 2x100bp on Illumina Nextseq2000
See Stewart-Morgan, K.R., et al., (Repli-ATAC 2023), van den Berg et al.,(scEdU-seq, 2022), Salmen et al.,(VASA-seq 2022), Zeller et al., (ChiC-seq 2022)
For Repli-ATAC, Bigwigs files were created using deepTools bamCoverage and bamCompare, with options `--binSize 15000 and a normalization scale factor was applied for spike in normalization. For VASA-seq, scEdU-seq, ChiC-seq,  see  Zeller et al, (ChIC-seq, 2022), van den Berg et al.,(scEdU-seq, 2022), Salmen et al.,(VASA-seq 2022)
Assembly: GRCh38 (Gencode) and dm6 (flybase)
Supplementary files format and content: BigWIg files (15Kb binned) & deduplicated single cell count tables (tsv.gz) & bed files (15kb bins)

growth_protocol: Human TERT-RPE-1 cells (female) were cultured in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12, GlutaMAX™ supplement (DMEM, Gibco) containing 10% Fetal Bovine Serum (FBS, Sigma Aldrich) and 100 U/mL penicillin/streptomycin (Gibco) at 37°C in 5% C02

extract_protocol:
Stewart-Morgan, K.R., et al., (Repli-ATAC 2023), van den Berg et al.,(scEdU-seq, 2022), Salmen et al.,(VASA-seq 2022) & Zeller et al., (ChIC-seq, 2022)
Stewart-Morgan, K.R., et al., (Repli-ATAC 2023), van den Berg et al.,(scEdU-seq, 2022), Salmen et al.,(VASA-seq 2022), Zeller et al., (ChIC-seq, 2022)
repli-ATAC-seq, scEdU-seq, VASA-seq & ChIC-seq

treatment_protocol: RPE1 cells were treated for inficiated times with 1 µM of dTAG-v1 molecule (Bio-Techne).

value: hTERT-immortalized retinal pigment epithelial cells

value: dTAG


title: VASAseq on Asynch. RPE1 CAF1 30hrs DSMO treated cells replicate 1

value: DMSO


title: VASAseq on Asynch. RPE1 CAF1 2hrs dTAG treated cells replicate 1


title: dpb4D_Input rep5

description: add tetO_MT

value: Input


title: mcm22A_H3K9me3_eSPAN rep2

description: add tetO_MT


title: VASAseq on Asynch. RPE1 CAF1 2hrs DSMO treated cells replicate 1


title: VASAseq on Asynch. RPE1 CAF1 30hrs dTAG treated cells replicate 2


title: mcm22A_H3K9me3_ChIP rep2

description: add tetO_MT


title: VASAseq on Asynch. RPE1 CAF1 30hrs DSMO treated cells replicate 2


title: mcm22A_dpb4D_BrdU rep5

description: add tetO_MT


title: mcm22A_BrdU rep6

description: add tetO_MT


title: VASAseq on Asynch. RPE1 CAF1 2hrs dTAG treated cells replicate 2


title: VASAseq on Asynch. RPE1 CAF1 2hrs DSMO treated cells replicate 2


title: mcm22A_H3K9me3_eSPAN rep1

description: add tetO_MT


title: mcm22A_Input rep6

description: add tetO_MT


title: mcm22A_H3K9me3_ChIP rep1

description: add tetO_MT


title: Uninf+IFN-γ

description:
Uninf_IFNg_GKO
10x Chromium Single Cell 3’ Library v3.1 chemistry, NextSeq 2000 P3 Kit (100 cycles).


title: VASAseq on Asynch. RPE1 WT cells plate 6


title: mcm22A_Input rep5

description: add tetO_MT


title: VASAseq on Asynch. RPE1 WT cells plate 3


title: WT_H3K9me3_eSPAN rep2

description: add tetO_MT

value: WT


title: VASAseq on Asynch. RPE1 WT cells plate 2


title: VASAseq on Asynch. RPE1 WT cells plate 1


title: WT_Input rep6

description: add tetO_MT


title: WT_H3K9me3_ChIP rep2

description: add tetO_MT


title: VASAseq on Asynch. RPE1 WT cells plate 4


title: WT_H3K9me3_eSPAN rep1

description: add tetO_MT


title: H3K27me3 ChIC on 30hrs dTAG treated RPE1


title: WT_H3K9me3_ChIP rep1

description: add tetO_MT


title: H3K27me3 ChIC on DMSO treated RPE1


title: H3K9me3 ChIC on 30hrs dTAG treated RPE1


title: H3K9me3 ChIC on 2hrs dTAG treated RPE1


title: WT_BrdU rep5

description: add tetO_MT


title: WT_BrdU rep6

description: add tetO_MT


title: WT_Input rep5

description: add tetO_MT


title: H3K27me3 ChIC on 2hrs dTAG treated RPE1


title: pob3_mcm2_dpb4_H3K4me3_eSPAN rep2


title: VASAseq on Asynch. RPE1 WT cells plate 5


title: mcm22A_BrdU rep5

description: add tetO_MT


title: pob3_mcm2_dpb4_H3K4me3_ChIP rep2


title: 2hr dTAG treated RPE1 clone6 double pulse scEdU-seq plate 2


title: pob3_mcm2_dpb4_Input rep2


title: 2hr dTAG treated RPE1 clone6 double pulse scEdU-seq plate 1


title: pob3_mcm2_dpb4_H3K4me3_eSPAN rep1


title: H3K9me3 ChIC on DMSO treated RPE1


title: pob3_mcm2_dpb4_H3K4me3_ChIP rep1


title: DMSO treated RPE1 clone6 double pulse scEdU-seq plate 2


title: DMSO treated RPE1 clone6 double pulse scEdU-seq plate 1


title: DMSO treated RPE1 double pulse scEdU-seq plate 4


title: pob3_mcm2_dpb4_Input rep1


title: DMSO treated RPE1 double pulse scEdU-seq plate 2


title: DMSO treated RPE1 double pulse scEdU-seq plate 3


title: pob3_BrdU rep2


title: 2hr dTAG treated RPE1 double pulse scEdU-seq plate 4


title: pob3_H3K4me3_eSPAN rep2


title: DMSO treated RPE1 double pulse scEdU-seq plate 1


title: 2hr dTAG treated RPE1 double pulse scEdU-seq plate 3


title: H3K9me3 ChIC on 15hrs dTAG treated RPE1


title: pob3_H3K4me3_ChIP rep1


title: pob3_Input rep2


title: 2hr dTAG treated RPE1 double pulse scEdU-seq plate 1


title: 10min dTAG treated RPE1 double pulse scEdU-seq plate 4


title: pob3_H3K4me3_eSPAN rep1


title: pob3_mcm2_dpb4_BrdU rep2


title: 2hr dTAG treated RPE1 double pulse scEdU-seq plate 2


title: pob3_Input rep1


title: pob3_BrdU rep1


title: 10min dTAG treated RPE1 double pulse scEdU-seq plate 3


title: mcm22A_dpb4D_H3K56ac_eSPAN rep2


title: 10min dTAG treated RPE1 double pulse scEdU-seq plate 2


title: H3K27me3 ChIC on 15hrs dTAG treated RPE1


title: pob3_mcm2_dpb4_BrdU rep1


title: mcm22A_dpb4D_H3K56ac_ChIP rep2


title: pob3_H3K4me3_ChIP rep2


title: 10min dTAG treated RPE1 double pulse scEdU-seq plate 1


title: mcm22A_dpb4D_BrdU rep4


title: ATAC-seq dTAG


title: mcm22A_dpb4D_Input rep4


title: mcm22A_dpb4D_H3K56ac_eSPAN rep1


title: repli-ATAC EdU Input CTRL replicate 3 Mature chromatin DMSO


title: mcm22A_dpb4D_BrdU rep3


title: mcm22A_dpb4D_H3K56ac_ChIP rep1


title: repli-ATAC EdU Input CTRL replicate 3 Nascent chromatin dTAG


title: mcm22A_dpb4D_Input rep3


title: repli-ATAC EdU Input CTRL replicate 3 Nascent chromatin DMSO


title: mcm22A_H3K56ac_eSPAN rep2


title: mcm22A_H3K56ac_ChIP rep2


title: repli-ATAC EdU Input CTRL replicate 2 Mature chromatin DMSO


title: mcm22A_BrdU rep4


title: repli-ATAC EdU Input CTRL replicate 2 Nascent chromatin dTAG


title: mcm22A_Input rep4


title: repli-ATAC EdU Input CTRL replicate 2 Nascent chromatin DMSO


title: mcm22A_H3K56ac_eSPAN rep1


title: repli-ATAC EdU Input CTRL replicate 1 Mature chromatin dTAG


title: mcm22A_H3K56ac_ChIP rep1


title: repli-ATAC EdU Input CTRL replicate 1 Mature chromatin DMSO


title: repli-ATAC EdU Input CTRL replicate 1 Nascent chromatin dTAG


title: mcm22A_BrdU rep3


title: repli-ATAC EdU Input CTRL replicate 1 Nascent chromatin DMSO


title: mcm22A_Input rep3


title: ATAC-seq DMSO


title: dpb4D_H3K56ac_eSPAN rep2


title: dpb4D_H3K56ac_ChIP rep2


title: repli-ATAC EdU Input CTRL replicate 3 Mature chromatin dTAG