title: THP-1, DMSO, 72 hours, replicate 2

description: stranded RNA-seq

data_processing:
The Salmon-tximport-DESeq2 pipeline was used for differential gene expression analysis. Salmon (version 1.2.1) was first used to quantify transcript abundance. A Salmon index was generated using the GENCODE (version 34) genome annotation, and subsequently the `salmon quant` tool was used with the `--validateMappings` option to calculate transcript abundances. Then, the R package tximport was used to import Salmon results into R and perform data preparation. The `summarizeToGene` function was used to collapse transcript abundances to the gene level. From here, the R package DESeq2 was used for differential gene expression analysis. We first extracted normalized counts for each RNA-seq experiment using DESeq2 by running the `estimateSizeFactors` function and then the `counts` function with option `normalized=TRUE`. For each individual experiment, the DESeq2 statistical model was modified based on the experimental design.
The STAR-featureCounts-REMBRANDTS-limma pipeline for differential RNA stability analysis. RNA-seq sequencing reads were first aligned to the hg38 reference genome using STAR5 (version 2.7.3a). Then, featureCounts was used to quantify intron and exon level counts. Finally, REMBRANDTS was used to calculate mRNA stability as previously described (PMID: 29030541; https://github.com/csglab/REMBRANDTS). Briefly, the package estimates a gene-specific bias function that is subtracted from Δexon–Δintron calculations to provide unbiased mRNA stability measurements. To assess differential RNA stability changes, we used limma, which was designed for microarray experiments and serves a similar function to DESeq2, though it supports negative values (relevant for RNA stability analysis). The model designs used here are analogous to the designs for differential expression analysis and based on the experiment design.
iPAGE run and downstream analysis pipeline for Gene Ontology analysis (see https://github.com/abearab/pager).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DESeq2 normalized count values for each Sample

extract_protocol:
At 72 hours, RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian kit (Takara) due to retirement of the ScriptSeq v2 kit. Total RNA was depleted using the RiboGone module included with the SMARTer kit. All RNA-seq libraries were assessed on a BioAnalyzer 2100 (Agilent) for library quantification and quality control and sequenced on an Illumina HiSeq 4000 using single-end, 50–base pair sequencing.

treatment_protocol: Cells were seeded into 6-well plates at 100,000 cells/mL in duplicate or triplicate and were treated with decitabine (100 nM on days 0, 1 and 2) or DMSO.


title: HL-60, decitabine, 72 hours, replicate 2

status: Public on Jan 13 2023

type: SRA

city: Palo Alto

first: Abolfazl

last: Arab

state: CA

address: 3160 Porter Dr

country: USA

institute: Arc Institute

description: 3' RNA-seq

library_source: transcriptomic

data_processing:
The Salmon-tximport-DESeq2 pipeline was used for differential gene expression analysis. Salmon (version 1.2.1) was first used to quantify transcript abundance. A Salmon index was generated using the GENCODE (version 34) genome annotation, and subsequently the `salmon quant` tool was used with the `--validateMappings` option to calculate transcript abundances. Then, the R package tximport was used to import Salmon results into R and perform data preparation. The `summarizeToGene` function was used to collapse transcript abundances to the gene level. From here, the R package DESeq2 was used for differential gene expression analysis. We first extracted normalized counts for each RNA-seq experiment using DESeq2 by running the `estimateSizeFactors` function and then the `counts` function with option `normalized=TRUE`. For each individual experiment, the DESeq2 statistical model was modified based on the experimental design.
The STAR-featureCounts-REMBRANDTS-limma pipeline for differential RNA stability analysis. RNA-seq sequencing reads were first aligned to the hg38 reference genome using STAR5 (version 2.7.3a). Then, featureCounts was used to quantify intron and exon level counts. Finally, REMBRANDTS was used to calculate mRNA stability as previously described (PMID: 29030541; https://github.com/csglab/REMBRANDTS). Briefly, the package estimates a gene-specific bias function that is subtracted from Δexon–Δintron calculations to provide unbiased mRNA stability measurements. To assess differential RNA stability changes, we used limma, which was designed for microarray experiments and serves a similar function to DESeq2, though it supports negative values (relevant for RNA stability analysis). The model designs used here are analogous to the designs for differential expression analysis and based on the experiment design.
iPAGE was used to perform gene ontology analysis (see https://github.com/abearab/pager).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DESeq2 normalized count values for each Sample

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
At 72 hours, RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and assessed on a BioAnalyzer 2100 (Agilent) for library quantification and quality control. RNA-seq libraries were sequenced on an Illumina HiSeq 4000 using single-end, 50–base pair sequencing.

treatment_protocol: Cells were seeded into 6-well plates at 100,000 cells/mL in duplicate and were treated with decitabine (100 nM on days 0, 1 and 2), RG3039 (2 uM on day 0), both drugs or DMSO.

tag: cell line

tag: cell type

value: cancer cell line

tag: genotype

value: WT

tag: treatment

value: decitabine

tag: time

value: 72 hours


title: HL-60, decitabine + RG3039, 72 hours, replicate 1

description: 3' RNA-seq

value: decitabine + RG3039


title: HL-60, decitabine + RG3039, 72 hours, replicate 2

description: 3' RNA-seq


title: HL-60 RNA, DMSO, 72 hours, replicate 2

data_processing:
The adapters in the sequencing reads were removed using cutadapt87 (v3.1) with options ‘— trimmed-only -m 15 -a AGATCGGAAGAGCAC‘. The PCR duplicates in the reads were collapsed using CLIPflexR88 (v0.1.19). The UMIs for each read were extracted using UMI-tools 89 (v1.1.1) with the options ‘extract—bc-pattern=NN‘ for the 5’ end and options ‘extract—3prime—bc-pattern=NNNNN‘ for the 3’ end. Reads corresponding to rRNA and other non-nuclear mRNA were removed by aligning out the reads using Bowtie290 (v2.4.2) on a depletion reference (rRNA, tRNA and mitochondrial RNA sequences). This depletion reference was built from the hg38 noncoding transcriptome (Ensembl91,92 version 96). The reads that did not align to the depletion reference were aligned to the hg38 mRNA transcriptome (Ensembl version 96) using Bowtie2 with options ‘— sensitive—end-to-end—norc‘. The mRNA transcriptome was built using the cDNA longest CDS reads of Homo sapiens downloaded from the Ensembl release version. The resulting reads were converted to BAM files and then sorted using samtools (v1.11). The duplicate reads in the sorted files were removed using UMI-tools (v1.1.1) with options ‘dedup‘.
Ribolog was used to compare translational efficiency across conditions93 (https://github.com/goodarzilab/Ribolog). Briefly, Ribolog applies a logistic regression to model individual Ribo-seq and RNA-seq reads in order to provide estimates of logTER (i.e., logFC in TE) and its associated p-value across the coding transcriptome.
Assembly: hg38
Supplementary files format and content: tab-delimited text file that includes gene level differential translational efficiency.
Library strategy: Ribo-seq

molecule: total RNA

extract_protocol:
At 72 hours, approximately 10x10^6 cells were lysed in ice cold polysome buffer (20 mM Tris pH 7.6, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide) supplemented with 1% v/v Triton X-100 and 25 U/mL Turbo DNase (Invitrogen). The lysates were triturated through a 27G needle and cleared for 10 min at 21,000 g at 4°C. The RNA concentrations in the lysates were determined with the Qubit RNA HS kit (Thermo). Lysate corresponding to 15 µg RNA was diluted to 200 µl in polysome buffer and digested with 0.75 µl RNaseI (Epicentre) for 45 min at room temperature. The RNaseI was then quenched by 5 µl SUPERaseIN (Thermo).     Monosomes were isolated using MicroSpin S-400 HR (Cytiva) columns, pre-equilibrated with 3 mL polysome buffer per column. 100 µl digested lysate was loaded per column (two columns were used per 200 µl sample) and centrifuged 2 min at 600 g. The RNA from the flow through was isolated using the RNA Clean and Concentrator-25 kit (Zymo). In parallel, total RNA from undigested lysates were isolated using the same kit.    Ribosome protected footprints (RPFs) were gel-purified from 15% TBE-Urea gels as 17-35 nt fragments. RPFs were then end-repaired using T4 PNK (New England Biosciences) and pre-adenylated barcoded linkers were ligated to the RPFs using T4 Rnl2(tr) K227Q (New England Biosciences). Unligated linkers were removed from the reaction by yeast 5’-deadenylase (New England Biosciences) and RecJ nuclease (New England Biosciences) treatment. RPFs ligated to barcoded linkers were pooled, and rRNA-depletion was performed using riboPOOLs (siTOOLs) per the manufacturer’s recommendations. Linker-ligated RPFs were reverse transcribed with ProtoScript II RT (New England Biosciences) and gel-purified from 15% TBE-Urea gels.
Ribosome protected footprints (RPFs) were gel-purified from 15% TBE-Urea gels as 17-35 nt fragments. RPFs were then end-repaired using T4 PNK (New England Biosciences) and pre-adenylated barcoded linkers were ligated to the RPFs using T4 Rnl2(tr) K227Q (New England Biosciences). Unligated linkers were removed from the reaction by yeast 5’-deadenylase (New England Biosciences) and RecJ nuclease (New England Biosciences) treatment. RPFs ligated to barcoded linkers were pooled, and rRNA-depletion was performed using riboPOOLs (siTOOLs) per the manufacturer’s recommendations. Linker-ligated RPFs were reverse transcribed with ProtoScript II RT (New England Biosciences) and gel-purified from 15% TBE-Urea gels. cDNA was then circularized with CircLigase II (Epicentre) and used for library PCR. First, a small-scale library PCR was run supplemented with 1X SYBR Green and 1X ROX (Thermo) in a qPCR instrument. Then, a larger scale library PCR was run in a conventional PCR instrument, performing a number of cycles that resulted in ½ maximum signal intensity during qPCR. Library PCR was gel-purified from 8% TBE gels and sequenced on a SE50 run on an Illumina HiSeq4000.cDNA was then circularized with CircLigase II (Epicentre) and used for library PCR. First, a small-scale library PCR was run supplemented with 1X SYBR Green and 1X ROX (Thermo) in a qPCR instrument. Then, a larger scale library PCR was run in a conventional PCR instrument, performing a number of cycles that resulted in ½ maximum signal intensity during qPCR. Library PCR was gel-purified from 8% TBE gels and sequenced on a SE50 run on an Illumina HiSeq4000.

treatment_protocol: Cells were seeded into 6-well plates at 100,000 cells/mL in duplicate and were treated with decitabine (100 nM at 0, 24 and 48 hours) or DMSO.

value: DMSO


title: THP-1, DMSO, 72 hours, replicate 1

description: stranded RNA-seq


title: THP-1, decitabine, 72 hours, replicate 3

description: stranded RNA-seq


title: OCI-AML3, DMSO, 72 hours, replicate 3

description: stranded RNA-seq


title: THP-1, decitabine, 72 hours, replicate 2

description: stranded RNA-seq


title: THP-1, decitabine, 72 hours, replicate 1

description: stranded RNA-seq


title: OCI-AML3, DMSO, 72 hours, replicate 2

description: stranded RNA-seq


title: OCI-AML2, DMSO, 72 hours, replicate 3

description: stranded RNA-seq


title: OCI-AML3, decitabine, 72 hours, replicate 2

description: stranded RNA-seq


title: OCI-AML3, decitabine, 72 hours, replicate 1

description: stranded RNA-seq


title: HL-60, DMSO, 72 hours, replicate 2

description: 3' RNA-seq


title: OCI-AML3, DMSO, 72 hours, replicate 1

description: stranded RNA-seq


title: MOLM-14, DMSO, 72 hours, replicate 3

description: stranded RNA-seq


title: OCI-AML2, DMSO, 72 hours, replicate 1

description: stranded RNA-seq


title: OCI-AML3, decitabine, 72 hours, replicate 3

description: stranded RNA-seq


title: THP-1, DMSO, 72 hours, replicate 3

description: stranded RNA-seq


title: MOLM-14, DMSO, 72 hours, replicate 2

description: stranded RNA-seq


title: OCI-AML2, decitabine, 72 hours, replicate 3

description: stranded RNA-seq


title: OCI-AML2, DMSO, 72 hours, replicate 2

description: stranded RNA-seq


title: MOLM-14, DMSO, 72 hours, replicate 1

description: stranded RNA-seq


title: OCI-AML2, decitabine, 72 hours, replicate 2

description: stranded RNA-seq


title: MOLM-14, decitabine, 72 hours, replicate 2

description: stranded RNA-seq


title: IFNb 2h 6 RNA

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

data_processing:
Reads were trimmed applying the tool TrimGalore version 0.4.4_dev. The adaptor sequence “AGATCGGAAGAGC” (Illumina TruSeq, Sanger iPCR; auto-detected) as well as 3 bp from the 5’ end and 15 bp from the 3’ end were removed. In addition, sequences that became shorter than 18 bp (after quality trimming) were removed using TrimGalore’s default settings.
Reads were mapped to the mm10 transcriptome build GRC38.93 from ENSEMBL using boWTie version 0.12.7 with its standard options.
Reads falling into genes were counted from BAM files applying a suited R/Bioconductor workflow (function SummarizeOverlaps with mode ‘Union’). Duplicated reads were removed. For ribosomal footprinting samples, reads in the coding part of genes (CDS) were counted, for total RNA samples reads in the whole gene body were counted.
Genome_build: mm10, GRCm38.93
Supplementary_files_format_and_content: Counts of deduplicated reads overlapping CDS for ribosome-protected libraries or gene bodies for total RNA in each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
Cells were collected, washed and lysed in Polysome lysis buffer (20 mM Tris-HCl, pH 7.4, 120 mM KCl, 5 mM MgCl2, 14 mM β-mercaptoethanol, 1% NP-40, 100 µg/ml CHX, 1x complete protease inhibitor cocktail (Roche), 100 u/ml RNase Inhibitor (Thermo Fisher)). Lysates containing 40 μg of total RNA were treated with 100 U of RNaseI (Ambion) for 45 min and stopped by addition of 50 U of SUPERaseIn (Ambion). Samples were centrifuged through 25% sucrose cushion at 100,000 rpm for 1 h and the pelleted RNA was extracted with the Direct-Zol RNA Miniprep kit (Zimo). Ribosomal RNA was depleted with the Gold Ribo-Zero kit (Illumina). Resulted RNA samples were resolved by electrophoresis in a 15% NOVEX TBE-Urea gel (Thermo Fisher). Gel slices including ribosome footprints corresponding to a fuzzy band of the 26-34 nt size range were cut out from the gel, crushed by centrifugation in 0.5 ml gel-breaker tubes (Segmatic) and extracted in 0.5 ml 10 mM Tris-HCl pH 7.0 by incubation for 15 min at 70°C. RNA was recovered by precipitation with isopropanol in presence of 0.3 M sodium acetate pH 5.5 and 20 μg Glycoblue (Thermo Scientific). For the parallel total mRNA sequencing, we used the same NSC lysates prepared as described above at the amount of 20 μg of total RNA. RNA was extracted with phenol/chloroform as described (Faye et al. 2014). RNA samples were treated with 3 U of TURBO DNase (Ambion) for 15 min at 37°C. RNA was again extracted with phenol/chloroform and recovered with ethanol precipitation in the presence of 0.3 m sodium acetate pH 5.2. Ribosomal RNA was depleted with the Gold Ribo-Zero kit (Illumina). After depletion 80 ng of each RNA sample was used to synthesized cDNA and make a library using the NEBNext Ultra Directional RNA library kit for Illumina (NEB).
Recovered RNA was dephosphorylated with T4 PNK (NEB) in the absence of ATP. Indexed libraries were generated using the SMARTer smRNA-Seq kit for Illumina (Takara).

treatment_protocol: Cells were treated with vehicle or IFN-β 48 hours after seeding and incubated at 37°C 25% CO2 for the corresponding incubation time. Then, NSCs were incubated for 5 min with 0.1 mg/ml CHX at 37°C 25% CO2.

tag: strain

tag: age

value: 8-12 weeks

value: Neural stem cells

tag: tissue

value: Ventricular-subventricular zone


title: KG-1, DMSO, 72 hours, replicate 2

description: stranded RNA-seq


title: HL-60, DMSO, 72 hours, replicate 2

description: stranded RNA-seq

data_processing:
The Salmon-tximport-DESeq2 pipeline was used for differential gene expression analysis. Salmon (version 1.2.1) was first used to quantify transcript abundance. A Salmon index was generated using the GENCODE (version 34) genome annotation, and subsequently the `salmon quant` tool was used with the `--validateMappings` option to calculate transcript abundances. Then, the R package tximport was used to import Salmon results into R and perform data preparation. The `summarizeToGene` function was used to collapse transcript abundances to the gene level. From here, the R package DESeq2 was used for differential gene expression analysis. We first extracted normalized counts for each RNA-seq experiment using DESeq2 by running the `estimateSizeFactors` function and then the `counts` function with option `normalized=TRUE`. For each individual experiment, the DESeq2 statistical model was modified based on the experimental design.
The STAR-featureCounts-REMBRANDTS-limma pipeline was used for differential RNA stability analysis. RNA-seq sequencing reads were first aligned to the hg38 reference genome using STAR5 (version 2.7.3a). Then, featureCounts was used to quantify intron and exon level counts. Finally, REMBRANDTS was used to calculate mRNA stability as previously described (PMID: 29030541; https://github.com/csglab/REMBRANDTS). Briefly, the package estimates a gene-specific bias function that is subtracted from Δexon–Δintron calculations to provide unbiased mRNA stability measurements. To assess differential RNA stability changes, we used limma, which was designed for microarray experiments and serves a similar function to DESeq2, though it supports negative values (relevant for RNA stability analysis). The model designs used here are analogous to the designs for differential expression analysis and based on the experiment design.
Pathway enrichment for differential expression and RNA stability data was assessed using iPAGE (see https://github.com/abearab/pager).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include DESeq2 normalized count values for each Sample

extract_protocol:
At 6, 72 and 120 hours, RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the ScriptSeq v2 kit (EpiCentre). Total RNA was depleted using RiboZero Gold (EpiCentre) and purified using the MinElute RNA kit (Qiagen). All RNA-seq libraries were assessed on a BioAnalyzer 2100 (Agilent) for library quantification and quality control and sequenced on an Illumina HiSeq 4000 using single-end, 50–base pair sequencing.


title: KG-1, decitabine, 72 hours, replicate 2

description: stranded RNA-seq


title: HL-60, DMSO, 72 hours, replicate 1

description: stranded RNA-seq


title: HL-60, decitabine, 72 hours, replicate 1

description: stranded RNA-seq


title: MOLM-14, decitabine, 72 hours, replicate 1

description: stranded RNA-seq


title: OCI-AML2, decitabine, 72 hours, replicate 1

description: stranded RNA-seq


title: HL-60, DMSO, 6 hours, replicate 2

description: stranded RNA-seq

value: 6 hours


title: HL-60, decitabine, 6 hours, replicate 2

description: stranded RNA-seq


title: MOLM-14, decitabine, 72 hours, replicate 3

description: stranded RNA-seq


title: HL-60, DMSO, 6 hours, replicate 1

description: stranded RNA-seq


title: HL-60, DMSO, 120 hours, replicate 2

description: stranded RNA-seq

value: 120 hours


title: HL-60, DMSO, 120 hours, replicate 1

description: stranded RNA-seq


title: KG-1, DMSO, 72 hours, replicate 1

description: stranded RNA-seq


title: KG-1, DMSO, 72 hours, replicate 3

description: stranded RNA-seq


title: KG-1, decitabine, 72 hours, replicate 3

description: stranded RNA-seq


title: KG-1, decitabine, 72 hours, replicate 1

description: stranded RNA-seq


description: stranded RNA-seq


title: NT2-Input, rep1

city: Umeå

first: Yuri

last: Schwartz

address: Building 6K, 6L  University Hospital Area

department: Molecular Biology

country: Sweden

institute: Umeå University

library_source: genomic

data_processing:
For all fastq.gz files that do not start with "TB-2458" base calling and quality score assignment were done with HiSeq Control Software 2.2.58/RTA 1.18.64. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite.
For all fastq.gz files started with "TB-2458" base calling and quality score assignment were done with NovaSeq Control Software 1.6.0/RTA v3.4.4. The Bcl to FastQ conversion was performed using bcl2fastq_2.20.0.422 from the CASAVA software suite.
The sequencing reads were aligned to human GRCh38/hg38 reference genome using bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) set to --phred33 -p 8
Reads with MAPQ scores less than 10 were removed using samtools (v1.3.1) (Li et al., 2009) view command and the following parameters: -h -b -@ 8 -q 10
Significantly enriched regions were identified from the filtered bowtie2 alignments with MACS2 (v2.1.2) (Zhang et al., 2008) callpeak command using the following parameters: -f BAM -g hs --broad --min-length 1000 -B --nomodel --extsize 180 --SPMR
Assembly: hg38
Supplementary files format and content: Read count profiles in BedGraph format, broadPeak

molecule: genomic DNA

source_name: cultured cells

growth_protocol: NTERA-2 (NT2-D1 ATCC® CRL-1973™), TIG-3 (see (Cameron et al., 2018) for more details), 293T (ATCC® CRL-3216™) and Hela (ATCC® CCL-2™) were cultured in high-glucose DMEM (Gibco) supplemented with 10% fetal bovine serum (Sigma), 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate (Gibco), and 1.5 g/liter sodium bicarbonate (Sigma) at 37 °C in an atmosphere of 5% CO2. F10 cells (clone of KBM7-1-55-S2-24 cell line) were cultured in Iscove’s Modified Dulbecco’s Medium (1X) (Gibco) supplemented with 15% of heat inactivated serum (Sigma), 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate (Gibco), and 3.024 g/liter sodium bicarbonate at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
Live cells were crosslinked with 1% formaldehyde for 10 min at 37C. Soluble chromatin was prepared and immunoprecipitation performed as described in Kahn et al. Nucleic Acids Res. 2016. 44:10132-10149
Libraries were prepared with NEBNext Ultra II FS DNA Library Prep Kit for Illumina (E7805) and NEBNext Multiplex Oligos for Illumina Index Primers Set 1 (E7335) according to manufacturer’s instructions. Briefly, 2 ng of ChIP DNAs were fragmented for 20 minutes to the average length of 180bp, followed by adaptor ligation and 8 cycles of PCR amplification.
HiSeq2500, 1x51 setup, 'HiSeq Rapid SBS Kit v2' chemistry
NovaSeq SP,100bp read length, v1 sequencing chemistry

treatment_protocol: no treatment

tag: chip antibody


title: NT2-Input, rep2


title: TIG3-SUZ12, rep1

value: Cell signaling, #3737P


title: HL-60, decitabine, 6 hours, replicate 1

description: stranded RNA-seq


title: preDC H24-HIVAztNvp

city: Paris

first: Philippe

last: Benaroch

address: 12, rue Lhomond

department: INSERM U932 Immunity and Cancer

country: France

institute: Institut Curie

library_source: transcriptomic single cell

data_processing:
A concatenated reference sequence for human and HIV is built with Cellranger mkref
Sample demultiplexing, alignment, UMI counting, and cell calling is performed using CellRanger v2.1.0 with default parameters
Gene-cell expression matrices for all samples are imported and merged with Seurat v2.3.4. Cells with <200 detected genes (UMI>0) and genes detected in <3 cells across the samples are filtered out
Expression values are normalized and log-transformed (log((xij+1)/nj) where x is the UMI count of gene j in cell i and nj is the total UMI count for cell j); normalized gene expression values are centered and scaled (z-score)
Gene expression dispersion is computed with mean.var.plot method from Seurat v2.3.4; genes whose expression ranges in [0.1,8] and dispersion >1 are defined as highly variable
PCA is computed on the highly variable genes
Clustering is performed on the top 22 PCs with Waltman and van Eck algorithm using k=30 neighbors and resolution r=0.3
Assembly: GRCh38
Assembly: NC_001802
Supplementary files format and content: tsv and mtx files containing the gene/cell expression matrices (UMI counts)

source_name: PBMC

growth_protocol: Isolated pre-DC were cultured in Xvivo medium (Lonza)

extract_protocol:
Chromium Single Cell 3' Reagent Kits v2 (10X Genomics)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured with HIV-1 NL-AD8 complemented or not with Vpx (plasmid VPX-any-VPR),with or without azidothymidine (Azt, 25µM) and neverapin (Nvp, 5µM), for either 12 or 24 hours

value: preDC

tag: time point (hour)

value: HIV-1 NL-AD8 complemented with Vpx + AZT/NVP


title: NT2-SUZ12, rep1


title: NT2-MEL18, rep1


title: NT2-SUZ12, rep2


title: TIG3-MEL18, rep2


title: NT2-MEL18, rep2


title: TIG3-MEL18, rep1


title: preDC H24-CpGA

value: CpG-A


title: TIG3-Input, rep1


title: TIG3-Input, rep2


title: preDC H24-HIV

value: HIV-1 NL-AD8 complemented with Vpx


title: HL-60, decitabine, 120 hours, replicate 2

description: stranded RNA-seq


title: preDC H24-mock

value: mock medium


title: HL-60, decitabine, 120 hours, replicate 1

description: stranded RNA-seq

value: cancer cell line


title: preDC H12-mock


title: preDC H12-CpGA


title: HLA-ABC low screen control

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Library strategy: CRISPR-seq
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
The RSA algorithm was used to rank the genes for which targeting sgRNA were significantly enriched in the sorted populations compared to the control unsorted populations grown in parallel.
Supplementary_files_format_and_content: Guide Counts file

source_name: lymphoblast

growth_protocol: K562 cells were cultured in RPMI-1640 supplemented with 2 mM Glutamax, 100 IU/mL Penicillin, 100 μg/mL Streptomycin and 10% HI-FCS in 5% CO2 at 37ºC

extract_protocol:
Genomic DNA was extracted using Puregene Core Kit A, Qiagen
Two rounds of PCR, with the second round primers containing adaptors for Illumina sequencing.

treatment_protocol: K-562 Cas9 cells were infected with the pooled lentiviral genome-wide sgRNA library at a multiplicity of infection of 0.3. Infected cells were selected with 1 μg/mL puromycin for 72 hr, commencing 48 hr after transduction. Cells were pulsed with 1ng/mL or 25ng/mL of IFNg 24h prior to FACS sorting and enriched for MHC-I positive cells (high screen) and MHC-I low (low screen) cells, respectively, by two rounds of sorting at day 18 and 25 (positive) and day 7 and 15 (low) following transduction with the sgRNA library.

tag: crispr library

value: Bassik Human CRISPR KO Library


title: HLA-ABC low screen

tag: facs antibody

value: APC-conjugated anti-human HLA-A,B,C specific antibody (W6/32, Biolegend)


title: preDC T0


title: HTO WT young and others

description: hashtags.txt.gz

data_processing:
Single-cell libraries were filtered using the 10x index-hopping-filter 1.0.1
quantified using kallisto|bustools’s lamanno workflow (kb_python 0.26.3) against GRCm38 with annotations from ENSEMBL (version 102)
Hashtag libraries were quantified using CITE-seq-Count 1.4.5.
Count matrices were read into scanpy 1.6.0 and concatenated
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrices with annotations for genes and cells

source_name: Subventricular Zone, Olfactory Bulb

extract_protocol:
After animal sacrifice, the vSVZ, striatum, rostral migratory stream and olfactory bulb was isolated. These latter three tissues were pooled together and referred to as Rest of the Brain (RoB). Tissues were processed as described previously (Llorens-Bobadilla et al. 2015) and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. For sorting, we size selected the vSVZor RoB cells and excluded for doublets, dead cells and CD45+/Ter119+/O4+cells as recently described (Kalamakis et al. 2019). We sorted vSVZ eYFP+ cells and GLAST+cells. From the RoB, cells that were eYFP+and eYFP-/PSANCAM low were sorted.
Cells were labelled with Hashtags oligos (HTO) using the Cell Hashing protocol from Biolegend (TotalSeq-A). All the sorted cells were pooled on the same tube and processed in the Chromium Next GEM Chip G using Chromium Next GEM Single Cell 3’ v3.1.Gene expression libraries were prepared following the manufacturer’s protocol (Chromium Next GEM Single Cell 3’ v3.1) at the Single-cell open lab at DKFZ. Each condition (TiCY and TiCY-IFNAGRKO young and old) was processed on a separate 10X reaction. Hashtags libraries were processed according to the manufacturer’s instruction (Biolegend).

treatment_protocol: Tamoxifen (TAM) injection was done in three days as follows: two doses daily of 1mg of tamoxifen in 100 uL of a solution of 10 mg/ml of TAM in EtOH 10% diluted on sunflower seed oil. TiCY young mice were injected with TAM at 10 weeks old and were sacrificed 6 weeks afterwards. TiCY old mice (71 weeks old), TiCY-IFN(A/G)-R young (7 weeks old) and old mice (85 and 98 weeks old) were injected with TAM and were sacrificed 9 weeks afterwards.

value: wildtype

value: TiCY

value: 16 weeks

value: various

value: SVZ, olfactory bulb, RMS, Striatum


title: HTO KO young

description: hashtags.txt.gz

value: IFNAGR KO

value: TiCY-IFNAGRKO


title: Ifng_wt_hto_udi1

description: hashtags.txt.gz


title: HTO KO old

description: hashtags.txt.gz


title: HTO WT old

description: hashtags.txt.gz

value: 80 weeks


title: KO young

description:
raw_counts.mtx.gz
genes.txt.gz
barcodes.txt.gz


title: WT old


title: TIG3-SUZ12, rep2

value: Cell signaling, #3737P


title: preDC H12-HIV

value: preDC


title: KO old


title: WT young


title: S014549

type: RNA

city: Edinburgh

first: Max

last: Bylesjo

state: Scotland

address: BioCube 1, Edinburgh BioQuarter, 13 Little France Road

country: United Kingdom

institute: Fios Genomics Ltd

hyb_protocol: The samples were hybridized to Clariom S Human Array Plates according to standard Affymetrix GeneTitan protocol

scan_protocol: Array plates were scanned using the Affymetrix GeneTitan Scanner with AGCC and exported as CEL files

data_processing: CEL files were imported into R and the input data was normalised using RMA, resulting in normalised expression levels in log base 2

label: biotin

label_protocol: Samples were labeled with biotin using the GeneChip WT Plus Reagent Kit according to the manufacturer's instructions.

extract_protocol: RNA was extracted from whole blood collected with PAXgene RNA tubes according to the manufacturer's recommendations

tag: individual (patient id)

value: 3 month follow-up after rejection

tag: center

value: RCSI

tag: patient group

value: PL Chronic graft injury (> 3 yrs post-transplant)

tag: gender

value: M

value: blood

value: PBMC


title: S028184

value: AUH

value: PL Acute rejection < 3 yrs post-transplant


title: S027084

value: FT Acute rejection < 3 yrs post-transplant


title: S028769

value: CUB


title: S020270

value: F


title: BE2C Combination-12h-biological replicate 1

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

description: Gene expression data from BE2C cells

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically using the data extraction protocol included in the software. After importing the CEL files, the data were summarized and normalized using the RMA method implemented in the Affymetrix® Expression Console™ (1.3.1.187).

source_name: Human cancer cell line

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit according to the manufactuer's instruction.

growth_protocol: BE2C cells were cultured in standard RPMI medium at 37C in 5% CO2 incubator.

extract_protocol: RNA were extracted by using Rnesay kit from QIAGEN according to instruction.

treatment_protocol: BE2C cells were treated with DMSO, 5uM of EPZ6437, 5nM of YM155 or combination of EPZ6438 with YM155 for 8 hours, and 12 hours.

value: neuroblastoma


title: S023946


title: S022275


title: BE2C EPZ6438-12h-biological replicate 1

description: Gene expression data from BE2C cells


title: BE2C Combination-8h-biological replicate 2

description: Gene expression data from BE2C cells


title: BE2C YM155-12h-biological replciate 2

description: Gene expression data from BE2C cells


title: S015709


title: S008840


title: S023518


title: BE2C Combination-8h-biological replicate 1

description: Gene expression data from BE2C cells


title: S019832


title: S027337

value: UBR


title: S007488

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: BE2C Combination-12h-biological replicate 2

description: Gene expression data from BE2C cells


title: S025045


title: S023500


title: BE2C EPZ6438-12h-biological replicate 2

description: Gene expression data from BE2C cells


title: BE2C YM155-8h-biological replciate 2

description: Gene expression data from BE2C cells


title: S021241


title: S019498

value: NANT

value: FT Long-term (> 3 yrs) rejection-free survival


title: BE2C YM155-8h-biological replciate 1

description: Gene expression data from BE2C cells


title: S012757


title: Mice lacking Gal-7 (Lgals7-/-)

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
We performed 75-nt paired-end uencing using an Illumina Hi2500 platform
QC and alignment of the short-read uences against the reference genome were performed with the ShortRead and Rsubread R/Bioconductor packages respectively.
the number of reads mapped to each gene on the basis of the UCSC.mm10. Known Gene database was counted, reported, and annotated using the GenomicFeatures, GenomicAlignments and org.Mm.eg.db packages.
To identify genes differentially expressed between tumors, we used the DE2-test on the basis of the normalized number of reads mapped to each gene.
Genome_build: UCSC (mm10)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin papillomas

extract_protocol:
RNA from mouse skin papillomas (3 pooled tumors for each genotype including WT, Lgals7-/- and Tg46) were isolated and purified using TRIzol reagent (Thermo Fisher Scientific) and RNeasy mini kit (Qiagen). RNA concentration and integrity were determined on an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNAs were processed for RNA- library construction using the Tru RNA Sample Preparation Kit v2 (Illumina) according to manufacturer protocol.

treatment_protocol: The two-stage carcinogenesis model (DMBA/TPA) was employed to induce skin tumors in WT, Lgals7-/- and Tg46 transgenic mice.

value: Skin papillomas

value: DMBA/TPA-induced carcinogenesis


title: Mice overexpressing Gal-7 in keratinocyte cells

value: Tg46 transgenic


title: BE2C EPZ6438-8h-biological replicate 2

description: Gene expression data from BE2C cells


title: S018211

value: 3 month follow-up after rejection


title: BE2C YM155-12h-biological replciate 1

description: Gene expression data from BE2C cells


title: BE2C EPZ6438-8h-biological replicate 1

description: Gene expression data from BE2C cells


title: S019861


title: S020554


title: Wild-type mice (with Gal-7 endogenous expression)

value: Wild-type


title: S014496

value: M

value: blood


title: S019533

value: PBMC


title: BE2C DMSO-biological replicate 1

description: Gene expression data from BE2C cells

value: DMSO


title: S003445

value: AUH

value: FT Acute rejection < 3 yrs post-transplant


title: ICB-2006_5nM VNX + MCLi

first: Dylan

last: Sheerin

address: 1G Royal Parade

institute: WEHI

data_processing:
Fastq files were QC'd using fastQC
QC'd fastq files were aligned to the GRCh38 human reference reference genome using the Rsubread align function
Gene counts were quantified using featureCounts in R
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes gene count information for each sample

source_name: CD4+ T cells

extract_protocol:
RNA extraction was performed using the Isolate II RNA mini kit according to manufacturer’s instruction
An input of 100 ng of total RNA was prepared and indexed for illumina sequencing using the TruSeq RNA sample Prep Kit with RiboGlobin depletion as per manufacturer’s instruction. The indexed libraries were pooled and diluted to 1.5 pM for paired end sequencing (2 x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit as per manufacturer’s instructions.

treatment_protocol: Total CD4+ T cells from PLWH were cultured overnight in RF10 plus 1 U/ml IL-2 and 1 mM raltegravir to rest, and 3x106 cell aliquots treated with 1 mM venetoclax (Selleck Chemicals) or a matched percentage of DMSO diluent for 24 hours

value: CD4+ T cells

value: 5nM VNX + MCLi

value: 24h post-treatment


title: ICB-2006_DMSO


title: PRA011_10nM MCLi

value: 10nM MCLi


title: ICB-2006_PMA/PHA

value: PMA/PHA


title: BE2C DMSO-biological replicate 2

description: Gene expression data from BE2C cells

value: neuroblastoma


title: S003736

value: PL Acute rejection < 3 yrs post-transplant

value: F


title: S018257

value: RCSI


title: S020036

value: 3 month follow-up after rejection


title: ICB-2013_PMA/PHA


title: S019799


title: PRA006_PMA/PHA


title: PRA003_100nM VNX

value: 100nM VNX


title: S023333

value: Baseline

value: PL Long-term (> 3 yrs) rejection-free survival

value: M


title: S017044

value: CUB

value: FT Stable < 3 yrs post-transplant

value: blood

value: PBMC


title: PRA003_PMA/PHA

value: CD4+ T cells


title: PRA003_DMSO

value: DMSO

value: 24h post-treatment


title: S018378

value: UBR

value: Non-transplanted corneal disease


title: S003583

value: AUH

value: PL Acute rejection < 3 yrs post-transplant


title: ICB-2006_10nM VNX + MCLi

value: 10nM VNX + MCLi


title: S015281

value: F


title: PRA011_10nM VNX + MCLi


title: S020106

value: FT Long-term (> 3 yrs) rejection-free survival


title: S016361

value: Baseline

value: PL Stable < 3 yrs post-transplant


title: PRA003_10nM MCLi

value: 10nM MCLi


title: ICB-2006_100nM VNX + MCLi

value: 100nM VNX + MCLi


title: ICB-3147_PMA/PHA

value: PMA/PHA


title: ICB-2013_100nM VNX + MCLi


title: PRA011_100nM VNX

value: 100nM VNX


title: PRA003_5nM VNX + MCLi

value: 5nM VNX + MCLi


title: ICB-3147_10nM VNX

value: CD4+ T cells

value: 10nM VNX


title: ICB-3147_DMSO

value: DMSO

value: 24h post-treatment


title: ICB-3147_5nM VNX + MCLi


title: PRA003_10nM VNX


title: S015133

value: RCSI

value: FT Stable < 3 yrs post-transplant

value: M

value: blood

value: PBMC


title: S022185

value: AUH

value: Non-transplanted corneal disease


title: ICB-3147_100nM VNX


title: S018882

value: Baseline

value: CUB

value: PL Long-term (> 3 yrs) rejection-free survival

value: F


title: S016574

value: PL Acute rejection < 3 yrs post-transplant


title: S017871

value: NANT

value: FT Long-term (> 3 yrs) rejection-free survival


title: ICB-2006_10nM MCLi

value: CD4+ T cells

value: 10nM MCLi


title: ICB-3147_5nM VNX

value: 5nM VNX

value: 24h post-treatment


title: PRA011_10nM VNX

value: 10nM VNX


title: S021140

value: PL Stable < 3 yrs post-transplant


title: ICB-2006_100nM VNX

value: 100nM VNX


title: ICB-2013_5nM VNX + MCLi

value: 5nM VNX + MCLi


title: S028192

value: RCSI

value: M

value: blood

value: PBMC


title: S018406

value: Baseline

value: UBR

value: FT Stable < 3 yrs post-transplant


title: S025022

value: FT Acute rejection < 3 yrs post-transplant

value: F


title: ICB-2013_10nM MCLi

value: CD4+ T cells


title: PRA003_5nM VNX


title: S015842

value: PL Long-term (> 3 yrs) rejection-free survival


title: PRA003_100nM VNX + MCLi

value: 100nM VNX + MCLi


title: S023104

value: AUH

value: PL Acute rejection < 3 yrs post-transplant


title: S017470

value: CUB

value: FT Long-term (> 3 yrs) rejection-free survival


title: PRA006_100nM VNX + MCLi

value: 24h post-treatment


title: S018965


title: S017928

value: Healthy adult volunteer


title: S021169

value: FT Chronic graft injury (> 3 yrs post-transplant)

value: M


title: S023545

value: blood

value: PBMC


title: S026165

value: Baseline

value: NANT


title: S023434


title: S016604

value: UBR


title: ICB-2013_10nM VNX + MCLi

value: 10nM VNX + MCLi


title: S025141


title: PRA011_PMA/PHA

value: CD4+ T cells

value: PMA/PHA


title: ICB-2006_10nM VNX

value: 10nM VNX


title: S015345

value: F


title: ICB-3147_10nM MCLi

value: 10nM MCLi


title: S027380

value: AUH

value: PL Acute rejection < 3 yrs post-transplant


title: PRA011_5nM VNX

value: 5nM VNX

value: 24h post-treatment


title: PRA003_10nM VNX + MCLi


title: ICB-2013_DMSO

value: DMSO


title: S020467

value: CUB

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: ICB-3147_100nM VNX + MCLi

value: 100nM VNX + MCLi


title: S023792

value: Baseline

value: PL Stable < 3 yrs post-transplant

value: blood

value: PBMC


title: S025482

value: NANT

value: Non-transplanted corneal disease

value: M


title: S015065

value: UBR

value: F


title: ICB-2013_10nM VNX

value: CD4+ T cells

value: 10nM VNX


title: ICB-2006_5nM VNX

value: 5nM VNX


title: PRA011_100nM VNX + MCLi

value: 24h post-treatment


title: PRA006_5nM VNX + MCLi

value: 5nM VNX + MCLi


title: S020701

value: AUH

value: FT Long-term (> 3 yrs) rejection-free survival


title: PRA006_10nM VNX


title: S035007

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: ICB-3147_10nM VNX + MCLi

value: 10nM VNX + MCLi


title: S017748

value: Baseline

value: Healthy adult volunteer


title: PRA006_10nM VNX + MCLi


title: S019649

value: CUB

value: blood

value: PBMC


title: PRA006_DMSO

value: DMSO


title: ICB-2013_5nM VNX


title: S016823

value: RCSI

value: FT Acute rejection < 3 yrs post-transplant

value: M


title: PRA006_10nM MCLi

value: CD4+ T cells

value: 10nM MCLi


title: S019982

value: UBR

value: Non-transplanted corneal disease


title: S025909

value: PL Acute rejection < 3 yrs post-transplant


title: S024104

value: FT Long-term (> 3 yrs) rejection-free survival

value: F


title: S015956

value: AUH


title: S020240

value: Baseline

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: S015099


title: PRA006_5nM VNX

value: 5nM VNX

value: 24h post-treatment


title: PRA006_100nM VNX

value: 100nM VNX


title: PRA011_5nM VNX + MCLi

value: 5nM VNX + MCLi


title: PRA011_DMSO

value: DMSO


title: S020894

value: PL Long-term (> 3 yrs) rejection-free survival

value: blood

value: PBMC


title: S025624

value: RCSI

value: FT Acute rejection < 3 yrs post-transplant

value: M


title: ICB-2013_100nM VNX

value: CD4+ T cells


title: S017125

value: Healthy adult volunteer


title: CUTandRUN_220310_K562-CAS-IgG

data_processing:
library strategy: CUT&RUN
Bcl2fastq was used for demultiplexing and conversion of BCL files to FastQ files
The CUT&RUN tools software was used for trimming, aligning and peak calling. The software implements Trimmomatic v0.39 followed by Kseq for trimming and bowtie2 v2.2.9 for alignment.
Peak calls are from MACS v2.2.7.1 as imlemented by CUT&RUN tools.
Assembly: Hg19
Supplementary files format and content: broadPeak, except for INPUT

extract_protocol:
Cells were resuspended in Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1 x Roche complete EDTA-free protease inhibitor). Cells were bound to activated Concanavalin A beads. Bead-bound cells were resuspended in Anitbody Buffer (Wash Buffer supplemented with 2 mM EDTA and 0.05% Digitonin) and incubated with the antibody for 2h at room temperature. Samples were washed in Digitonin Buffer (Wash Buffer supplemented with 0.05% Digitonin) then incubated in Digitonin Buffer with pAG-MNase enzyme (cell signaling) for 1h at room temperature. Samples were washed. Then MNase was activated by the addition of CaCl2 (50 μL of Digitonin Buffer supplemented with 4mM CaCl2). Samples incubated at 1h at 37ºC. DNA digestion was stopped by STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.1% Digitonin, 100 μg/mL RNAse A, 50 μg/mL Glycogen) and incubated at 37ºC for 1h. DNA was purified with MinElute PCR purification Kit (Qiagen).
Sequencing libraries were prepared from eluted DNA using Rubicon ThruPLEX DNA-seq kit.

value: Human CML

value: WT

tag: cut&run antibody


title: S018012

value: Baseline

value: UBR

value: FT Long-term (> 3 yrs) rejection-free survival


title: CUTandRUN_220310_K562-CAS-MLL1

tag: cell line


title: CUTandRUN_220310_K562-MEN1c4-KO-MLL1

tag: cell type

value: MEN1 KO


title: K562-MLL1-2ko-EZH2i-IFN-H3K4me3

data_processing:
library strategy: CUT&TAG
Bcl2fastq was used for demultiplexing and conversion of BCL files to FastQ files
The CUT&RUN tools software was used for trimming, aligning and peak calling. The software implements Trimmomatic v0.39 followed by Kseq for trimming and bowtie2 v2.2.9 for alignment.
Peak calls are from MACS v2.2.7.1 as imlemented by CUT&RUN tools.
Assembly: Hg19
Supplementary files format and content: broadPeak, except for INPUT

extract_protocol:
Nuclei were isoalted by permeabilisting cells in NE1 Buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl 0.5 mM spermidine, 0.1% Triton-X100, 20% glycerol, 1x Roche complete EDTA-free protease inhibitor) on ice for 10 minutes. Nuclei were resuspended in Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1 x Roche complete EDTA-free protease inhibitor). Nuclei were bound to activated Concanavalin A beads. Bead-bound nuclei were resuspended in Anitbody Buffer (Wash Buffer supplemented with 2 mM EDTA and 0.1% BSA) and incubated with the antibody for 2h at room temperature. Samples were washed in 300 Buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1 x protease inhibitor cocktail) then incubated in 300 Buffer with CUTANA pAG-Tn5 enzyme (EpiCypher) for 1h at room temperature. Samples were washed. Then Incubated in Tagmentation Buffer  (300 Buffer supplemented with 10 mM MgCl2) for 1h at 37ºC. Tagmentation was stopped by STOP Buffer (300 Buffer supplemented with 40 mM EDTA, 0.2% SDS, 400 μg/mL proteinase K) and incubated at 55ºC for 2h, then held at 4ºC overnight. DNA was purified with MinElute PCR purification Kit (Qiagen).
To amplify libraries, 21 μL of eluted DNA was mixed with 2 μL of a universal i5 primer, 2 μL of a uniquely barcoded i7 primer (Buenrostro, J.D. et al., Nature, 2015) and 25 μL of NEBNext HiFi 2X PCR Master Mix. The samples were amplified using the following cycling conditions: 72°C for 5 min (gap filling); 98°C for 30 s; 14 cycles of 98°C for 10 s and 63°C for 10 s; final extension at 72°C for 1 min and hold at 8 °C.

treatment_protocol: K562 Cas9 and KMT2A/B KO cells were pre-treated with 3uM EZH2i for 7 days +/- 48h 25ng/mL IFNg

tag: genotype

tag: cut&tag antibody


title: S016416

tag: time

value: CUB

value: FT Stable < 3 yrs post-transplant


title: S017071

value: F


title: K562-MLL1-2ko-EZH2i-H3K4me3

tag: treatment


title: K562-CAS-EZH2i-IgG


title: K562-CAS-EZH2i-IFN-H3K4me3


title: K562-CAS-EZH2i-H3K4me3


title: S017442


title: S016085

value: AUH


title: S019592

value: blood


title: K562-NT2-H3K4me3


title: S021601

value: PL Chronic graft injury (> 3 yrs post-transplant)

value: PBMC


title: K562-NT2-H2AK119


title: S030134

value: FT Acute rejection < 3 yrs post-transplant


title: K562-NT2-H3K27me3


title: S018241

value: RCSI

value: PL Long-term (> 3 yrs) rejection-free survival


title: S020765

value: M


title: S023068


title: S017546


title: K562-MTF2sgRNA-H3K4me3

value: Human CML


title: K562-AEBP2sgRNA-H3K4me3


title: K562-MTF2sgRNA-H2AK119


title: K562-MTF2sgRNA-H3K27me3


title: S023662


title: K562-AEBP2sgRNA-H3K27me3


title: S024720


title: K562-NT2-IgG

value: WT


title: K562-CAS-IgG


title: K562-PCGF1ko-H3K4me3


title: K562-PCGF1ko-H2AK119


title: K562-PCGF1ko-H3K27me3


title: S016473

value: Baseline


title: S015410

value: Non-transplanted corneal disease


title: K562-MEN1ko-H3K27me3


title: S015374

value: PL Stable < 3 yrs post-transplant


title: S020140


title: S021573

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: S017962


title: S021208


title: S019930


title: K562-MEN1ko-H3K4me3


title: K562-EEDko-H3K4me3

value: EEDko


title: K562-CAS-H3K4me3


title: K562-EEDko-H2AK119


title: S024776

value: CUB

value: FT Long-term (> 3 yrs) rejection-free survival


title: K562-CAS-H3K27me3


title: K562-INPUT

data_processing:
Bcl2fastq was used for demultiplexing and conversion of BCL files to FastQ files
Cutadapt v1.14 was used for trimming adapters
Alignment was performed with BWA-MEM v0.7.13
Peak calling was conducted using MACS2 with default parameters
Assembly: Hg19
Supplementary files format and content: broadPeak, except for INPUT

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 15 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine. Cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and protease inhibitors. Lysates were sonicated in a Covaris ultrasonicator to achieve a mean DNA fragment size of 500 bp. Samples were diluted 1:10 in modified  RIPA buffer (1% Triton X-100, 0.1% deoxycholate, 90 mM NaCl, 10 mM Tris-HCl, pH 8.0, and protease inhibitors) then pre-cleared with Protein A Dynabeads (Life Technologies). Chromatin was then incubated with pre-bound anti-H3K27me3-bead mixture rotating overnight at 4 °C. After washing, samples were eluted from beads in Elution Buffer 1 (50 mM Tris pH 8.0, 1% SDS, 10 mM DTT).  Eluates were diluted 1:20 in modified RIPA buffer , 10% was kept back as primary ChIP, and then pre-cleared with Protein A Dynabeads rotating overnight at 4 °C. Samples were washed and incubated with second pre-bound anti-H3K4me3-bead mixture and rotated again overnight at 4°C. Samples were washed and eluted in Elution Buffer 2 (1% SDS, 0.1 M NaHCO3).  Samples were reverse cross-linked overnight and purified with MinElute PCR purification kit (Qiagen).
Sequencing libraries were prepared from eluted DNA using Rubicon ThruPLEX DNA-seq kit.


title: K562-CAS-H2AK119


title: K562-SINGLE-H3K4me3


title: K562-SINGLE-H3K27me3


title: S014975


title: H9-DMSO-INPUT

growth_protocol: H9 cells were maintained in mTESR Plus medium on 1% Geltrex coated plates. The cells were routinely passaged using EDTA dissociation buffer in 1:8 ratio, in presence of 2mM Thiazovivin

extract_protocol:
Cells were fixed with 2mM DSG (Theromo Scientific) for 30min at room temperature followed by cross-linking with 1% formaldehyde (methanol free) for 15 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine. Cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and protease inhibitors. Lysates were sonicated in a Covaris ultrasonicator to achieve a mean DNA fragment size of 500 bp. Samples were diluted 1:10 in modified  RIPA buffer (1% Triton X-100, 0.1% deoxycholate, 90 mM NaCl, 10 mM Tris-HCl, pH 8.0, and  protease inhibitors) and incubated rotating with antibody for a minimum of 12 h at 4 °C.  Protein A Dynabeads (Life Technologies) were used to bind the antibody and associated chromatin. After washing and elution from the beads, samples were reverse cross-linked overnight and purified with MinElute PCR purification kit (Qiagen).
Sequencing libraries were prepared from eluted DNA using Rubicon ThruPLEX DNA-seq kit.

treatment_protocol: Pre-treated with DMSO, 1uM VTP50459, 3uM EZH2i or 1uM VTP50469 and 3uM EZH2 inhibitors for 5 days

value: Human ES

value: DMSO


title: K562-ReChIP-with-clear-H3K4me3


title: S024132

value: F

value: blood


title: H9-VTP-MLL1

value: VTP


title: K562-EEDko-H3K27me3


title: S015651

value: PBMC


title: S016803

value: AUH


title: S018114

value: RCSI

value: M


title: S021321

value: FT Stable < 3 yrs post-transplant


title: S030280

value: Baseline

value: Healthy adult volunteer


title: S028258


title: S015871

value: Non-transplanted corneal disease


title: S016444


title: S029177

value: UBR


title: S028196


title: S026707

value: PL Acute rejection < 3 yrs post-transplant


title: S025113


title: S015607

value: CUB


title: H9-Combo-MLL1

value: WT

value: EPZ+VTP


title: H9-EPZ-MLL1

value: Human ES

value: EPZ


title: NANOGP1_KD_Day9_DOX_Replicate_3

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

data_processing:
Sequencing files were analysed by FastQC v0.11.9. RNA-sequencing reads were trimmed using trim galore v0.4.2 software to remove the adaptor sequences. Using HISAT v2.0.5 and guided by the gene models from the Ensembl v70, trimmed reads were mapped to the human GRCh38 genome. Raw sequencing data was converted from .bam to .sam file type using Samtools, and .sam files were imported to Seqmonk software.
Genes from Ensembl v70 were quantiated based on the count of overlapping reads.  The data was corrected for the total size of each library and log2 transformed (log2RPM)
Assembly: GRCh38
Supplementary files format and content: A tab-separated file of log2RPM read counts per transcript. Fields are "Probe", "Chromosome", "Start", "End", "Probe Strand", "Ensembl ID", "Description", "log2 RPM"

source_name: Naive ESCs (CRISPRi Gen1B line)

growth_protocol: CRISPRi naïve ESCs were maintained in t2iLGö medium.

extract_protocol:
RNA was extracted using an RNeasy Mini Kit (Qiagen).
Indexed libraries were made using 0.5 μg RNA per sample with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® with the Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Multiplex Oligos for Illumina® (NEB).

treatment_protocol: CRISPRi was induced with 1 μM doxycycline.

value: Embryonic stem cells (ESCs)

value: Naive ESCs (CRISPRi Gen1B line)

tag: cell state

value: Naive

value: NANOGP1 CRISPRi

value: DOX

tag: time point

value: day 9

tag: replicate

value: replicate 3


title: NANOGP1_KD_Day9_DOX_Replicate_2

value: replicate 2


title: S018293

value: Baseline

value: RCSI

value: FT Acute rejection < 3 yrs post-transplant

value: M

tag: tissue

value: blood

value: PBMC


title: S018075

value: AUH

value: Non-transplanted corneal disease


title: NANOGP1_KD_Day9_DOX_Replicate_1

value: replicate 1


title: NANOGP1_KD_Day9_Replicate_2

value: Embryonic stem cells (ESCs)


title: H9-DMSO-MLL1

value: Human ES

value: WT

value: DMSO

tag: chip antibody


title: NANOGP1_KD_Day4_DOX_Replicate_3

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

value: NANOGP1 CRISPRi

value: DOX

value: day 4


title: NANOGP1_KD_Day9_Replicate_1

value: day 9


title: S029206

value: Baseline

value: UBR

value: F


title: NANOGP1_KD_Day4_Replicate_3

value: replicate 3


title: S017016

value: CUB

value: FT Chronic graft injury (> 3 yrs post-transplant)

value: blood

value: PBMC


title: NANOGP1_KD_Day4_DOX_Replicate_1

value: Embryonic stem cells (ESCs)

value: replicate 1


title: S017847

value: NANT


title: S022040

value: PL Long-term (> 3 yrs) rejection-free survival


title: NANOGP1_KD_Day4_Replicate_2

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

value: replicate 2


title: NANOGP1_KD_Day2_DOX_Replicate_3

value: NANOGP1 CRISPRi

value: DOX

value: day 2


title: NANOGP1_KD_Day9_Replicate_3

value: day 9


title: S017162

value: Baseline

value: AUH

value: Healthy adult volunteer

value: M


title: S025184

value: RCSI

value: FT Stable < 3 yrs post-transplant

value: F

value: blood


title: NANOGP1_KD_Day2_DOX_Replicate_2

value: Embryonic stem cells (ESCs)


title: NANOGP1_KD_Day2_Replicate_3

value: replicate 3


title: S017568

value: NANT

value: PBMC


title: S026194

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: NANOGP1_KD_Day2_Replicate_2

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

value: NANOGP1 CRISPRi

value: replicate 2


title: NANOGP1_KD_Day4_Replicate_1

value: day 4

value: replicate 1


title: NANOGP1_KD_Day2_Replicate_1

value: day 2


title: S016388

value: Baseline

value: CUB

value: PL Long-term (> 3 yrs) rejection-free survival


title: S017625

value: FT Long-term (> 3 yrs) rejection-free survival

value: F


title: S017984

value: RCSI

value: Non-transplanted corneal disease

value: M

value: blood


title: S029299

value: UBR

value: FT Acute rejection < 3 yrs post-transplant

value: PBMC


title: S016332


title: NANOGP1_KD_Day2_DOX_Replicate_1

value: Embryonic stem cells (ESCs)

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

value: NANOGP1 CRISPRi

value: DOX


title: S017780

value: Baseline

value: AUH


title: NANOGP1_KD_Day0_Replicate_1

value: day 0

value: replicate 1


title: S015530

value: CUB

value: PL Acute rejection < 3 yrs post-transplant

value: F


title: S031214

value: NANT

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: NANOGP1_KD_Day4_DOX_Replicate_2

value: day 4

value: replicate 2


title: NANOG_KD_Day9_DOX_Replicate_3

value: NANOG CRISPRi

value: day 9

value: replicate 3


title: NANOG_KD_Day9_DOX_Replicate_2

value: Embryonic stem cells (ESCs)

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive


title: S022665

value: Baseline

value: Non-transplanted corneal disease

value: M

value: blood

value: PBMC


title: S024076

value: CUB

value: FT Long-term (> 3 yrs) rejection-free survival


title: S019032

value: UBR

value: PL Stable < 3 yrs post-transplant

value: F


title: S006663

value: AUH

value: Healthy adult volunteer


title: S022637


title: NANOGP1_KD_Day0_Replicate_3

value: NANOGP1 CRISPRi

value: day 0


title: NANOG_KD_Day9_Replicate_3

value: Embryonic stem cells (ESCs)

value: NANOG CRISPRi

value: day 9

value: replicate 3


title: NANOG_KD_Day9_DOX_Replicate_1

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

value: DOX

value: replicate 1


title: S021395

value: Baseline

value: PL Acute rejection < 3 yrs post-transplant

value: M

value: blood

value: PBMC


title: S008102

value: CUB

value: PL Stable < 3 yrs post-transplant

value: F


title: NANOG_KD_Day9_Replicate_2

value: replicate 2


title: NANOG_KD_Day6_DOX_Replicate_3

value: Embryonic stem cells (ESCs)

value: day 6


title: NANOG_KD_Day9_Replicate_1

value: NANOG CRISPRi

value: day 9


title: NANOG_KD_Day6_DOX_Replicate_2

value: Naive ESCs (CRISPRi Gen1B line)


title: S013613

value: Non-transplanted corneal disease


title: NANOG_KD_Day6_Replicate_2

value: Naive


title: S006277

value: RCSI

value: FT Long-term (> 3 yrs) rejection-free survival


title: S007165

value: Baseline

value: AUH

value: Healthy adult volunteer


title: S003161

value: FT Chronic graft injury (> 3 yrs post-transplant)

value: blood

value: PBMC


title: S011761

value: CUB

value: M


title: S002656

value: FT Stable < 3 yrs post-transplant


title: S008496

value: PL Chronic graft injury (> 3 yrs post-transplant)


title: NANOG_KD_Day6_Replicate_1

value: Embryonic stem cells (ESCs)

value: NANOG CRISPRi

value: day 6

value: replicate 1


title: S003054

value: Non-transplanted corneal disease


title: S022693

value: NANT


title: NANOG_KD_Day4_DOX_Replicate_2

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

value: DOX

value: day 4

value: replicate 2


title: NANOG_KD_Day4_DOX_Replicate_1


title: NANOG_KD_Day4_Replicate_3

value: replicate 3


title: S003555

value: Baseline

value: AUH

value: F

value: blood

value: PBMC


title: NANOG_KD_Day4_Replicate_1

value: Embryonic stem cells (ESCs)


title: NANOG_KD_Day6_Replicate_3

value: NANOG CRISPRi


title: S010175

value: RCSI

value: Healthy adult volunteer


title: S013502

value: CUB

value: Non-transplanted corneal disease

value: M


title: NANOG_KD_Day6_DOX_Replicate_1

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

value: day 6

value: replicate 1


title: NANOG_KD_Day4_DOX_Replicate_3

value: DOX

value: day 4

value: replicate 3


title: S012790

value: Baseline

value: F


title: NANOG_KD_Day2_DOX_Replicate_3

value: day 2


title: S004459

value: AUH

value: blood

value: PBMC


title: S002811

value: PL Long-term (> 3 yrs) rejection-free survival


title: NANOG_KD_Day2_DOX_Replicate_2

value: Embryonic stem cells (ESCs)

value: NANOG CRISPRi

value: replicate 2


title: NANOG_KD_Day2_DOX_Replicate_1

value: Naive ESCs (CRISPRi Gen1B line)


title: S005106

value: FT Stable < 3 yrs post-transplant

value: M


title: NANOG_KD_Day2_Replicate_3

value: Naive


title: NANOG_KD_Day4_Replicate_2


title: NANOG_KD_Day0_Replicate_3

value: day 0


title: NANOG_KD_Day2_Replicate_1

value: replicate 1


title: NANOG_KD_Day0_Replicate_1


title: VTP50469  Rep 3

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the human genome (G1k V37) using HiSAT2 and reads were assigned to genes using htseq-count.
Differential expression was calculated using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene counts from htseq

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit. RNA concentration was quantified with a Qubit Fluorometer (Thermo Fisher Scientific).
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexigen).

treatment_protocol: Cells were treated with DMSO or 1uM VTP50469 for 7 days


title: VTP50469  Rep 2


title: S001465

value: CUB


title: S011197

value: Baseline


title: S012784


title: S000717

value: PL Stable < 3 yrs post-transplant

value: F


title: S009214

value: Non-transplanted corneal disease


title: S013642

value: blood


title: NANOG_KD_Day2_Replicate_2

value: day 2


title: S010223

value: UBR

value: Healthy adult volunteer

value: PBMC


title: VTP50469  Rep 1


title: S006781

value: RCSI

value: FT Long-term (> 3 yrs) rejection-free survival


title: K562.DMSO.3

value: DMSO


title: K562.DMSO.1


title: S000775

value: FT Stable < 3 yrs post-transplant

value: M


title: NANOG_KD_Day0_Replicate_2

value: Embryonic stem cells (ESCs)

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

value: NANOG CRISPRi

value: day 0

value: replicate 2


title: Cas Rep 1

tag: ko

value: Cas


title: Cas Rep 3


title: S005589

tag: individual (patient id)

value: Baseline

value: CUB

value: FT Acute rejection < 3 yrs post-transplant

value: F

value: blood


title: Cas Rep 2


title: K562.DMSO.2


title: S000410

tag: center

value: AUH

value: PBMC


title: PSIP KO Rep 3

value: PSIP KO


title: S014206

tag: patient group


title: S000588

value: FT Chronic graft injury (> 3 yrs post-transplant)

tag: gender


title: S010810

value: Healthy adult volunteer


title: S005838


title: S011915


title: S000703

value: PL Stable < 3 yrs post-transplant


title: PSIP KO Rep 1


title: PSIP KO Rep 2


title: MENIN KO Rep 3

value: MENIN KO


title: MENIN KO Rep 1


title: MENIN KO Rep 2


title: S004298

value: Non-transplanted corneal disease

value: M


title: EED KO Rep 3

value: EED KO


title: EED KO Rep 1


title: EED KO Rep 2


title: S008131


title: S002454

value: FT Stable < 3 yrs post-transplant


title: S000192


title: MENIN ChIP MENIN inh

description: 15 minutes with 1% Formaldehyde (Methanol free)

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the human genome (GRCh37) with BWA-mem
Peak calling was performed with MACS2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bed files of peaks called by MACS2

extract_protocol:
Cells were cross-linked at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine. Cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and protease inhibitors. Lysates were sonicated in a Covaris ultrasonicator to achieve a mean DNA fragment size of 500 bp. Samples were diluted 1:10 in modified  RIPA buffer (1% Triton X-100, 0.1% deoxycholate, 90 mM NaCl, 10 mM Tris-HCl, pH 8.0, and  protease inhibitors) and incubated rotating with antibody for a minimum of 12 h at 4 °C.  Protein A Dynabeads (Life Technologies) were used to bind the antibody and associated chromatin. After washing and elution from the beads, samples were reverse cross-linked overnight and purified with QIAquick PCR purification kits (Qiagen).
Sequencing libraries were prepared from eluted DNA using Rubicon ThruPLEX DNA-seq kit.

treatment_protocol: Menin inhibitor cells: treated with 1uM VTP50469 for 7 days

value: MENIN inhibitor

value: MENIN


title: Fvb_Suprabasal_Rep3

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description:
180629_180807_RNA-seq_results.gene.rpkm.xlsx
t02_180807

data_processing:
Demultiplex and convert to FastQ using bcl2fastq v2.20.0.422
Map to mm10 using Tophat 2.1.1
Calculate RPKM (Partek GS 7.0)
ANOVA comparison (Partek GS)
Genome_build: mm10
Supplementary_files_format_and_content: RPKM and ANOVA results in Excel format

source_name: Skin epidermis

extract_protocol:
Skin epidermis was dissected as described in Lichti et al., 2008, and then percoll gradient separation was employed to isolate the basal and suprabasal cells.
RNA libraries were prepared according to standard Illumina protocol (NEBNext Ultra II RNA Library Prep kit for Illumina; Cat# E7775)

value: Skin epidermis

value: Suprabasal

tag: dlx3 genotype

value: WT

tag: strain

value: Fvb/N

tag: age

value: neonate (p0-p2)


title: Fvb_Suprabasal_Rep4

description:
180629_180807_RNA-seq_results.gene.rpkm.xlsx
t04_180807

tag: cell type


title: Fvb_Suprabasal_Rep2

description:
180629_180807_RNA-seq_results.gene.rpkm.xlsx
s04_180629


title: S000894

value: Baseline

value: AUH

value: blood

value: PBMC


title: MENIN ChIP MENIN KO

tag: cell line


title: Fvb_Suprabasal_Rep1

description:
180629_180807_RNA-seq_results.gene.rpkm.xlsx
s03_180629


title: S002090

tag: time

value: PL Long-term (> 3 yrs) rejection-free survival

value: F


title: S002876

value: Non-transplanted corneal disease


title: Fvb_Basal_Rep4

description:
180629_180807_RNA-seq_results.gene.rpkm.xlsx
t03_180807

value: Basal


title: Fvb_Basal_Rep3

description:
180629_180807_RNA-seq_results.gene.rpkm.xlsx
t01_180807


title: S012475

value: CUB

value: FT Long-term (> 3 yrs) rejection-free survival

value: M


title: MENIN ChIP cas

value: Cas

value: MENIN


title: S010407

value: RCSI


title: S013071


title: Fvb_Basal_Rep2

description:
180629_180807_RNA-seq_results.gene.rpkm.xlsx
s02_180629

value: Skin epidermis

value: WT


title: S000184

value: Healthy adult volunteer


title: S011630

value: Baseline

value: FT Stable < 3 yrs post-transplant


title: Fvb_Basal_Rep1

description:
180629_180807_RNA-seq_results.gene.rpkm.xlsx
s01_180629

value: Fvb/N

value: neonate (p0-p2)


title: Dlx3WT_Suprabasal_Rep2

description:
190124_0203_rna-seq_results.gene.rpkm.xlsx
s04_190124

value: Suprabasal

value: mix of CD-1 and C57BL/6


title: Input for MENIN ChIP


title: SUZ12 ChIP MEN1 KO

description: Fixed with 2mM DSG for 30 minutes, followed by 15 minutes with 1% Formaldehyde (methanol free)

value: MENIN KO


title: SUZ12 ChIP control


title: Dlx3KO_Suprabasal_Rep2

description:
190124_0203_rna-seq_results.gene.rpkm.xlsx
s02_190124

value: KO


title: Dlx3KO_Basal_Rep2

description:
190124_0203_rna-seq_results.gene.rpkm.xlsx
s06_190124

value: Basal


title: Dlx3WT_Basal_Rep2

description:
190124_0203_rna-seq_results.gene.rpkm.xlsx
s08_190124


title: Dlx3WT_Basal_Rep1

description:
190124_0203_rna-seq_results.gene.rpkm.xlsx
s07_190124


title: Dlx3KO_Basal_Rep1

description:
190124_0203_rna-seq_results.gene.rpkm.xlsx
s05_190124


title: Input for SUZ12 ChIP


title: S012695

value: F

value: blood

value: PBMC


title: NANOGP1_KD_Day0_Replicate_2

value: Embryonic stem cells (ESCs)

value: Naive ESCs (CRISPRi Gen1B line)

value: Naive

tag: genotype

value: NANOGP1 CRISPRi

value: day 0

value: replicate 2


title: H3K4me3 ChIP control

description: 15 minutes with 1% Formaldehyde (methanol free)

value: Cas


title: Input for H3K4me3 ChIP


title: S009977

value: Baseline

value: AUH

value: FT Stable < 3 yrs post-transplant


title: S002433

value: RCSI

value: M


title: Dlx3WT_Suprabasal_Rep1

description:
190124_0203_rna-seq_results.gene.rpkm.xlsx
s03_190124

value: Skin epidermis

value: Suprabasal

value: WT

value: mix of CD-1 and C57BL/6

value: neonate (p0-p2)


title: H3K4me3 ChIP MEN1 KO

value: MENIN KO


title: Dlx3KO_Suprabasal_Rep1

description:
190124_0203_rna-seq_results.gene.rpkm.xlsx
s01_190124

value: KO


title: S003106

value: PL Stable < 3 yrs post-transplant

value: F

value: blood

value: PBMC


title: S012653

value: UBR

value: PL Long-term (> 3 yrs) rejection-free survival


title: HLA high screen control

tag: crispr library

value: Bassik Human CRISPR KO Library


title: S001893

value: Baseline

value: CUB

value: Healthy adult volunteer


title: HLA-ABC high screen

tag: facs antibody

value: APC-conjugated anti-human HLA-A,B,C specific antibody (W6/32, Biolegend)


title: S002301

value: AUH


title: S013558

value: Non-transplanted corneal disease

value: M


title: S009752

value: FT Stable < 3 yrs post-transplant


title: erythroblasts at mko-Bhet-9,biological rep3

city: Yangzhou

first: Fangfang

last: Wang

state: Jiangsu

address: No. 98 of Nantong Road

country: China

institute: Clinical medical college, Yangzhou university

description: Gene expression data of  erythroblasts fractionated from bone marrow of mko/Bhet-9 mice

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on Affymetrix Mouse Transcriptome Array 1.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: Total RNA was isolated from cells at indicated time point with Trizol.

value: erythroblasts

value: mko;Bhet


title: S002558

value: PL Stable < 3 yrs post-transplant


title: HLA-B high screen

value: APC-conjugated anti-human HLA-B specific antibody (REA143, Miltenyi Biotec)


title: erythroblasts at mko-4, biological rep3

description: Gene expression data of  erythroblasts fractionated from bone marrow of mko-4 mice

value: mko


title: erythroblasts at mko-Bhet-7,biological rep1

description: Gene expression data of  erythroblasts fractionated from bone marrow of mko/Bhet-7 mice


title: CTRL-1079-4_S15

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

description: PAC-seq as described in Routh et al, 2017

data_processing:
Raw reads were trimed using fastp
Trimed reads were aligned to the reference genome using bowtie2
PCR duplicates were removed using umi tools
Samtools were used to sort, convert and index alignment files
Deeptools were used to generate bigwig files
Assembly: GRCh38
Supplementary files format and content: bigwig files
Library strategy: PAC-seq

source_name: control fibroblasts ATCC CCD-1079Sk (CRL-2097)

growth_protocol: Fibroblasts  cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1%L-Glutamine, 1% Pen/Strep  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 17 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).

value: skin

value: fibroblasts

value: wild-type

tag: treatment


title: erythroblasts at mko-Bhet-8,biological rep2

description: Gene expression data of  erythroblasts fractionated from bone marrow of mko/Bhet-8 mice


title: ScRNA data of three myasthenic crisis patients [mixed sample]

city: Shanghai

first: Sushan

last: Luo

state: Shanghai

address: 12 Wulumuqi Rd (M), Jing'An, Shanghai

institute: Huashan Hospital

description:
10x Genomics
Combination file

data_processing:
The analysis of single-cell dataset was conducted in Scanpy (version 1.9.1) running on Python (version 3.8.13). The batch effect of different samples was adjusted using the “harmony_integrate” function in Scanpy. Doublet cells were detected and removed using the latest version of scvi-tools. And preprocessing and clustering were conducted according to the 3k PBMCs tutorial in Scanpy (https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html). RNA velocity was calculated in velocyto and scvelo using the bam file from raw data for pseudotime-trajectory analysis. After these, a recently published automated cell type annotation tool “Celltypist” was applied to help classify cell types in the PBMCs. Two MC related ScRNA-cell-prediction models were used to help annotate cell types in our data. One is the build-in high-resolution immune cell annotation model (Immune_All_Low.pkl) in the Celltypist, and the other is a transfer-learning model generated by Celltypist using a recent published MG ScRNA dataset (only the PBMCs dataset was used). The marker genes for different cell types had consulted those used in previously published high-quality ScRNA articles.
Assembly: GRCh38-3.0.0
Supplementary files format and content: h5ad

source_name: Peripheral Blood

extract_protocol:
For each myasthenic crisis (MC) participant, 2 ml venous blood was collected in EDTA anticoagulant tubes and transferred to the laboratory with ice two times. The first time point was the initiation of intubation or mechanical ventilation, and the second time point was 3 months after the crisis. PBMCs were isolated by density gradient centrifugation using the Ficoll-Paque medium. The cell viability should exceed 90% which was determined with trypan blue staining. An appropriate volume of cell suspension was calculated to contain ~13,000 cells for each sample.
The PBMCs were loaded onto the 10× Chromium Single Cell Platform (10X Genomics) (5' and V(D)J Enrichment) as described in the manufacturer’s protocol. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification, and library construction were all performed as per the manufacturer’s protocol. Qubit was used for library quantification before pooling. The final library pool was sequenced on the Illumina Hiseq platform using 150 base-pair paired-end reads. The cellranger pipeline (version 6.1.1) was applied to analyze the sequencing raw data, with references of the transcriptome (GRCh38-3.0.0) .

tag: tissue

value: Peripheral Blood

value: PBMCs

tag: subject status

value: myasthenia crisis patinet

value: WT

value: Immunosuppressive treatments


title: erythroblasts at wt-1, biological rep2

description: Gene expression data of  erythroblasts fractionated from bone marrow  of wt-1 mice

value: wt


title: CTRL-1079-3_S14


title: erythroblasts at wt-10, biological rep1

description: Gene expression data of  erythroblasts fractionated from bone marrow of wt-10 mice


title: CTRL-1079-2_S13


title: erythroblasts at mko-2, biological rep2

description: Gene expression data of  erythroblasts fractionated from bone marrow of mko-2 mice


title: S007036

value: Baseline

value: AUH

value: blood

value: PBMC


title: erythroblasts at wt-5, biological rep3

description: Gene expression data of  erythroblasts fractionated from bone marrow  of wt-5 mice

value: erythroblasts


title: erythroblasts at Bhet-4, biological rep3

description: Gene expression data of rythroblasts fractionated from bone marrow of Bhet-4 mice

source_name: erythroblasts fractionated from bone marrow of Bhet-4 mice

value: Bhet


title: S008437

value: CUB

value: Non-transplanted corneal disease

value: M


title: CPSF6-MUT-5_S3

source_name: patient-derived fibroblasts CPSF6 D535V missense

value: skin

value: fibroblasts

value: CPSF6 heterozgous de novo missense mutation (D535V)


title: S000991

value: PL Stable < 3 yrs post-transplant

value: F


title: CPSF6-MUT-4_S2


title: erythroblasts at Bhet-3, biological rep2

description: Gene expression data of  erythroblasts fractionated from bone marrow of Bhet-3 mice


title: S001436

value: FT Long-term (> 3 yrs) rejection-free survival


title: erythroblasts at Bhet-2, biological rep1

description: Gene expression data of erythroblasts fractionated from bone marrow of Bhet-2 mice


title: CPSF6-MUT-3_S1


title: erythroblasts at mko-1, biological rep1

description: Gene expression data of  erythroblasts fractionated from bone marrow of mko-1 mice

value: mko


title: UMN029_1_preEx

city: Minneapolis

first: Ralph

last: White

state: MN

address: 420 Delaware Street SE

institute: University of Minnesota

data_processing:
cellranger count (cellranger-6.0.1)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz - Barcode sequences correspond to column indices in the count matrix file (matrix.mtx.gz)
Supplementary files format and content: features.tsv.gz - Features correspond to row indices in the count matrix file (matrix.mtx.gz). For each feature, the feature ID and name are stored in the first and second column of the (unzipped) features.tsv.gz file, respectively. The third column identifies the type of feature, which will be one of Gene Expression, Antibody Capture, CRISPR Guide Capture, Multiplexing Capture, or CUSTOM, depending on the feature type.
Supplementary files format and content: matrix.mtx.gz - Sparse matrix file format containing raw counts for the rows and columns defined by features and barcodes, respectively.

source_name: blood

extract_protocol:
10X Genomics Cell Preparation
10X Genomics Library Construction

value: primary NK cells

value: Donor pre-expansion


title: UMN026_2_postEx_preInf

value: Donor post-expansion with NAM but pre infusion


title: UMN026_3_postEx_postInf

value: blood

value: Donor post-expansion, post infusion (sorted):has '-D' suffix


title: UMN029_2_postEx_preInf


title: UMN029_3_postEx_postInf


title: UMN026_4_recipient

value: Recipient, post infusion (sorted):has '-R' suffix


title: UMN029_4_recipient


title: S007653

value: Baseline

value: AUH

value: PL Long-term (> 3 yrs) rejection-free survival

value: PBMC


title: S010438


title: UMN019_4_recipient


title: UMN026_1_preEx


title: CPSF6-DEL-3_S6

source_name: patient-derived fibroblasts CPSF6 0.25mb deletion

value: skin

value: CPSF6 heterozgous deletion


title: UMN019_2_postEx_preInf


title: UMN019_1_preEx


title: CPSF6-DEL-2_S5

value: fibroblasts


title: S004698


title: PBMCspleen, mRNA-derived cDNA

city: Brisbane City

first: Namrata

last: Bhattacharya

state: Queensland

address: 2 George St

institute: Queensland University of Technology

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline with default settings (v3.0.1) and aligning to the GRCh38 human reference genome.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Blood

extract_protocol:
Cells were isolated form PBMCs and splenocytes of four patients (two healthy donors, HD1 18 years old male and HD2 61 years old female; two brain-dead donors, BD1 57 years old female, and BD2 58 years old female). CITE-seq using Hashtag Oligos (HTO) was then performed to pool samples into a single 10X Genomics channel for scRNAseq as described in Abidi et al. (Abidi et al. 2020). HTO binding was carried out according to the manufacturer's guidance (BioLegend, Total-seq B)
Basically, after thawing ,and cell washing, 1M cells were centrifuged and resuspended in 100uL PSE buffer (PBS/FBS/EDTA). Cells were incubated with 10ul human FcR blocking reagent for 10 min at 4°C. 1 uL of a Hashtag oligonucleotide (HTO) antibody (Biolegend) was then added to each sample and incubated at 4°C for 30 min. Cells were then washed in 1mL PSE, centrifuged at 500g for 5 min and resuspended in 200uL PSE . Cells were stained with 2uL DAPI, 60uM filtered and viable cells were sorted (ARIA).
Cells were checked for counting and viability then pooled and counted again. Cell viability was < 95%. Cells of HD1 Spleen were lost during the washing step and thus not used during further downstream processing. Cells were then loaded on 1 channel of Chromium Next Controller with 3’ single cell Next v3 kit (10x Genomics Inc. Pleasanton, CA). We then followed the supplier’s protocol CG000185 Rev C until library generation. For HTO library, we followed the protocol of 10x genomics 3’ feature barcode kit (PN-1000079) to generate HTO libraries.
310pM of pooled libraries were sequenced on a NOVAseq6000 instrument with a S1 (v1) flow-cell (Illumina Inc. San Diego, CA) at the genomic platform core facility on the basis of a placement agreement (Nantes, IRS-Un, France) . The program was runned as follows : Read1 29 cycles / 8 cycles (i7) /0 (i5)/Read2 93 cycles (Standard module, paired-end, 2 lanes).

value: Blood

value: Spleenocyte and PBMC

tag: library type

value: mRNA

tag: antibodies/tags


title: PBMCspleen, HTO-derived cDNA

library_source: other

molecule: protein

value: HTO

value: HD1 PBMC Hashtag 6/ anti-human Totalseq-B394641; HD2 PBMC Hashtag 2 / anti-human Totalseq-B394633; HD2 Spleen Hashtag 5/ anti-human Totalseq-B394639;BD1 PBMC Hashtag 9/ anti-human Totalseq-B394647; BD1 Spleen Hashtag 3/ anti-human Totalseq-B394635; BD2 PBMC Hashtag 10/ anti-human Totalseq-B394649; BD2 Spleen Hashtag 1/ anti-human Totalseq-B394631


title: UMN019_3_postEx_postInf

value: primary NK cells


title: TYK2 [S65]

first: Gaspard

last: Kerner

address: 25-28 rue du docteur roux

institute: Institut Pasteur

data_processing:
BAM files were converted to a raw count’s expression matrix using ‘featurecount’. Raw count data was normalized using DEseq2. The Ensembl IDs targeting multiple genes were collapsed (average), and a final data matrix gene was generated for downstream analysis. Gene set enrichment analysis (GSEA) was conducted based on the fold-change (pairwise analysis of stimulated vs non-stimulated sample) ranking against the Hallmark (HM) gene sets (http://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=H).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: T-cell blast

growth_protocol: T-blasts were induced from 2 million peripheral blood mononuclear cells (PBMCs; fresh or cryopreserved) in 2 ml ImmunoCult™-XF T Cell Expansion Medium (StemCell Technologies, 10981) supplemented with 10 ng/ml IL-2 (Gibco, PHC0023) and 1:40 diluted ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (StemCell Technologies, 10970). T-blasts were then cultured in ImmunoCult Medium with IL-2 for 2-3 weeks, before they were re-stimulated in the same manner.

extract_protocol:
Total RNA was isolated from cells using the Quick-RNA MicroPrep spin column kit (Zymogen, R1050), following manufacturer’s protocol. RNA was then submitted for RNA sequencing library preparation and deep-sequencing to Rockefeller University Genomics Core Facility.
RNA-sequencing was performed on the Illumina NovaSeq platform, with a read length of 100bp and read depth of 30-40 million reads. All FASTQ files passed QC and were aligned to reference genome GRCh38 using STAR (2.6.1d).

treatment_protocol: T-cell blasts were starved off IL-2 over-night. Then, they were stimulated with 50 ng/ml IL-12 (R&D Systems, CAT: 219-IL-005) or 100 ng/ml IL-23 (R&D Systems, Cat: 1290-IL) for 6 hours or with 2.5 ng/ml IL1ß (R&D Systems, CAT: 201-LB-005)- for 24 hours. Double stimulated cells were stimulated with IL-1ß for 18 hours and then with IL-23 and IL-1ß for 6 hours.

value: T-cell blast

value: Unstimulated


title: S008187

data_processing: CEL files were imported into R and the input data was normalised using RMA, resulting in normalised expression levels in log base 2

extract_protocol: RNA was extracted from whole blood collected with PAXgene RNA tubes according to the manufacturer's recommendations

tag: individual (patient id)

tag: center

value: CUB

value: PL Stable < 3 yrs post-transplant

value: F

value: blood


title: CPSF6-DEL-1_S4


title: S001328

value: Baseline

tag: patient group

tag: gender


title: S012786

value: RCSI

value: Healthy adult volunteer

value: PBMC


title: TYK2 P1104A [S93]


title: TYK2 P1104A [S105]


title: TYK2 P1104A [S92]


title: TYK2 P1104A [S81]


title: TYK2 P1104A [S69]


title: TYK2 P1104A [S104]


title: TYK2 P1104A [S68]


title: S007263

value: AUH

value: FT Acute rejection < 3 yrs post-transplant


title: RBM7,Rep,3,t60

city: Aarhus

first: Ross

middle: Andrew Alex

last: Cordiner

address: Universitetsbyen 81

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
Demultiplexing and quality control: Reads were demultiplexed using rtCLIP barcodes initially to identify RBP and biological rep using pyBarcodeFilter.py using options -m 1 -k (version 3.0). Next, umi_tools (version 0.5.5) was used to append UMI to header using the extract function with following options --bc-pattern=NNNXXXXNN --bc-pattern2=XXXXXXXXN --log extract.log . Another round of demultiplexing applying the BCBarcodes to identify timepoints from specific RBP biological replicates using pyBarcodeFilter.py with the following options -b$BCBarcodes.txt -m 1 -k –search reverse . Finally, trim_galore was used for QC using the following options --stringency 4 --phred33 --fastqc --illumina -a2 AGATCGGAAGAGC --clip_R1 4 --clip_R2 8 --three_prime_clip_R1 9 --three_prime_clip_R2 9 --trim1 (version 0.5.0)
Mapping and QC: Reads were mapped using hisat2 (version 2.1.0)  with the following options -t --rna-strandness FR --fr --phred33 -p 10 --new-summary --no-softclip --known-splicesite-infile . samtools (version 1.9) was used to sort, index and remove secondary reads.  umi_tools was used to remove PCR duplicates from the mapped reads using the dedup function with the following options --paired (version 0.5.5)
Making read1 and read2, and derivative cross-link and 3CLIP bigwig files: samtools (version 1.9) and bedtools (version v2.28.0) was used to extract read 1 and 2, and custom awk scripts were used to flip read2 strand identity. Custom awk scripts were also used to extract the cross-link site and 3CLIP from read1 and read2 bed files. Bedtools and bedGraphToBigWig (version 4) from UCSC tools were used to generate bigwig files. Bigwig files were scaled to the number of reads mapped to 30 rRNA genes.
Assembly: hg38

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (10 %FCS) supplemented with penicillin streptomycin, and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were lysed via sonication and RNA was extracted via immunoprecipitation of the relevant cross-linked RNA binding protein.
Standard iCLIP library construction was used with a few alterations from the original protocol (Konig et al. 2011) . iCLIP libraries were constructed from each UV cross-linked sample. As the adapters used in the first ligation reaction contained an inline barcode, all timepoints and controls for a given biological replicate were pooled after gel-extraction. Reverse transcription was performed on the pooled RNA using standard RtClip oligos that contained a 2nd in-line barcode which was used to identify the RBP and the biological replicate.

treatment_protocol: HeLa cells at 70% confluency were incubated with 100uM DRB, or the equivalent volume of organic solvent (DMSO) for 3 hours to pause RNAPII transcription. After 3 hours, the DRB block was released by aspirating the drug-containing media and replacing with fresh media. At the appropriate timepoint cells were UV cross-linked for 30 seconds and cells were scraped, pelleted and frozen at -80°C until required. Timepoint 0 (t00) samples were UV cross-linked immediately after 3 hours DRB incubation.

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 60 min


title: RBM7,Rep,3,t15

value: 15 min


title: RBM7,Rep,3,t20

value: 20 min


title: RBM7,Rep,3,t40

value: 40 min


title: TYK2 P1104A [S80]

value: T-cell blast


title: TYK2 P1104A [S116]

description: TYK2_P1104A_1_IL1b_2_5ng_ml_IL23_100ng_ml_S116


title: RBM7,Rep,3,t10

value: 10 min


title: TYK2 [S89]


title: TYK2 [S77]


title: TYK2 [S101]


title: S002784

source_name: PBMC

value: CUB

value: FT Long-term (> 3 yrs) rejection-free survival

value: F


title: RBM7,Rep,3,t05

value: 05 min


title: TYK2 P1104A [S117]

description: TYK2_P1104A_2_IL1b_2_5ng_ml_IL23_100ng_ml_S117


title: (irradiated) Rep 3

city: Haikou

first: Shakil

last: Ahmad

state: Hainan

address: Hainan University, Haikou, Hainan Province, 570228

department: School of Plant Protection

institute: Hainan University

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 low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to Drosophila genome assembly GCF_000806345.1_ASM80634v1(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/806/345/GCF_000806345.1_ASM80634v1/GCF_000806345.1_ASM80634v1_genomic.fna.gz) using HISAT2 with default parameters.
HTSeq v0.6.1p2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GCF_000806345.1_ASM80634v1
Supplementary_files_format_and_content: Tab-delimited text files include count and FPKM values for each sample

organism: Zeugodacus cucurbitae

growth_protocol: Hatched larvae from both irradiated and non-irradiated group were transferred to the artificial larval diet.Twenty individuals of 3rd instar from each replication of both irradiated and non-irradiated groups were collected and immediately frozen in liquid nitrogen and then stored at -80°C for RNA extraction.

extract_protocol:
Total RNA was extracted by using TRIzol (Invitrogen) according to the manufacturer's instructions.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated.

treatment_protocol: Under free oxygen, at 1.0 Gy/min, eggs of approximately 25 h old were irradiated with 60Co at the following doses: 0 Gy (control) and 50 Gy.

tag: developmental stage

value: 3rd instar larvae


title: S005165

value: Baseline

value: FT Stable < 3 yrs post-transplant

value: blood

value: PBMC


title: TYK2 [S113]


title: S016725

value: AUH

value: PL Acute rejection < 3 yrs post-transplant

value: M


title: S008848

value: RCSI


title: S003292

value: PL Stable < 3 yrs post-transplant


title: RBM7,Rep,3,t00

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 00 min


title: (irradiated) Rep 2


title: S000323

value: CUB


title: IL23R R381Q [S71]

value: T-cell blast

value: Unstimulated


title: (irradiated) Rep 1

value: 3rd instar larvae


title: S012903

value: Baseline

value: UBR

value: F


title: RBM7,Rep,3,DMSO

value: DMSO


title: RBM7,Rep,3,negative

value: WT


title: IL23R R381Q [S95]


title: (Non-irradiated) Rep 3


title: (Non-irradiated) Rep 2


title: IL23R R381Q [S83]


title: S006719

value: Non-transplanted corneal disease

value: blood

value: PBMC


title: IL23R R381Q [S107]


title: RBM7,Rep,2,t40

value: 40 min


title: S000877

value: PL Long-term (> 3 yrs) rejection-free survival


title: RBM7,Rep,2,t20

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: 20 min


title: (Non-irradiated) Rep 1


title: IL23R R381Q [S119]

description: IL23R_R381Q_2_IL1b_2_5ng_ml_IL23_100ng_ml_S119


title: IL23R R381Q [S70]


title: RBM7,Rep,2,t15

value: DRB

value: 15 min


title: S008876

value: CUB

value: M


title: RBM7,Rep,2,t60

value: 60 min


title: In-vitro Z.tritici strain Zt99, replicate 3

city: Harpenden

first: Daniel

last: Smith

state: Hertfordshire

address: West Common

department: IDE

institute: Rothamsted Research

data_processing:
Reads mapped using HiSat2 (v2.0.5)
Mapped reads counted using Subread FeatureCounts (v1.6.2)
Assembly: pangenome assembly: Pangenome_Zt_17I_IPO323_v3.fasta ; annotation: annotation_pangenomveV3_2.gtf (bespoke for this paper, data archived and included here)
Supplementary files format and content: FeatureCount gene counts: ztriticiPangenomePlantaCounts.txt

organism: Zymoseptoria tritici

source_name: in-vitro fungal culture

growth_protocol: in-vitro broth culture or in-planta wheat infections as described above

extract_protocol:
TRIzol (Invitrogen)
Illumina 100bp  paired-end reads

treatment_protocol: Sampling at log phase in vitro or at stated days post infection in-planta

tag: strain

tag: in-vitro growth phase

value: log phase growth

tag: in-vitro medium

value: Culture medium:YPD broth


title: In-vitro Z.tritici strain Zt99, replicate 1


title: IL23R R381Q [S94]

tag: cell type

value: T-cell blast


title: In-vitro Z.tritici strain Zt99, replicate 2


title: IL23R R381Q [S82]

tag: genotype


title: S011262

tag: time

value: Baseline

value: AUH

value: PL Stable < 3 yrs post-transplant

value: F


title: RBM7,Rep,2,t10

tag: cell line

value: 10 min


title: In-vitro Z.tritici strain Zt93, replicate 3


title: RBM7,Rep,2,t00

tag: treatment

value: 00 min


title: In-vitro Z.tritici strain Zt93, replicate 2


title: IL23R R381Q [S106]


title: RBM7,Rep,2,t05

value: HeLa

value: 05 min


title: S001971

value: Healthy adult volunteer

tag: tissue

value: blood

value: PBMC


title: IL12RB1 [S63]

value: Unstimulated


title: S010029

value: RCSI

value: Non-transplanted corneal disease

value: M


title: S014684

value: PL Acute rejection < 3 yrs post-transplant


title: S001831

value: CUB


title: IL23R R381Q [S118]

description: IL23R_R381Q_1_IL1b_2_5ng_ml_IL23_100ng_ml_S118

value: T-cell blast


title: In-vitro Z.tritici strain Zt92, replicate 3

value: log phase growth

value: Culture medium:YPD broth


title: RBM7,Rep,2,DMSO

value: Human papillomavirus-related endocervical adenocarcinoma

value: DMSO


title: S005311

value: Baseline

value: PL Stable < 3 yrs post-transplant

value: F


title: S002194


title: In-vitro Z.tritici strain Zt92, replicate 1


title: RBM7,Rep,1,t60

value: HeLa

value: DRB

value: 60 min


title: In-vitro Z.tritici strain Zt92, replicate 2


title: RBM7,Rep,1,t20

value: 20 min


title: IL12RB1 [S99]


title: S001236

value: FT Stable < 3 yrs post-transplant

value: blood

value: PBMC


title: IL12RB1 [S75]


title: RBM7,Rep,1,t40

value: 40 min


title: S006784

value: RCSI

value: PL Long-term (> 3 yrs) rejection-free survival

value: M


title: RBM7,Rep,2,negative

value: WT


title: IL12RB1 [S111]

description: IL12RB1_IL1b_2_5ng_ml_IL23_100ng_ml_S111

value: T-cell blast


title: In-vitro Z.tritici strain Zt88, replicate 3

value: log phase growth

value: Culture medium:YPD broth


title: In-vitro Z.tritici strain Zt88, replicate 2


title: HC10 [S10]

value: WT/WT

value: Unstimulated


title: In-vitro Z.tritici strain Zt93, replicate 1


title: S012210

value: Baseline

value: FT Acute rejection < 3 yrs post-transplant

value: F


title: RBM7,Rep,1,t15

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 15 min


title: In-vitro Z.tritici strain Zt88, replicate 1


title: IL12RB1 [S87]


title: S016545

value: UBR

value: Healthy adult volunteer

value: blood

value: PBMC


title: RBM7,Rep,1,t10

value: 10 min


title: HC10 [S34]

value: T-cell blast


title: HC10 [S22]


title: RBM7,Rep,1,t05

value: 05 min


title: In-vitro Z.tritici strain Zt80, replicate 3

value: log phase growth

value: Culture medium:YPD broth


title: In-vitro Z.tritici strain Zt80, replicate 2


title: S002024

value: CUB

value: FT Long-term (> 3 yrs) rejection-free survival

value: M


title: RBM7,Rep,1,t00

value: 00 min


title: HC10 [S46]

value: WT/WT


title: In-vitro Z.tritici strain Zt80, replicate 1