title: wildtype_K562_wt_LMNB1_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: LMNB1.
pADamID_22


title: C2.3

status: Public on Oct 20 2021

type: SRA

city: Colchester

first: Liudmila

last: Mikheeva

address: Wivenhoe Park

country: United Kingdom

institute: University of Essex

library_source: transcriptomic

data_processing:
Trimmed reads were aligned to Synechocystis sp. PCC 6803 genome (GCA_000009725.1) using TopHat v2.1.2 with Bowtie2 v2.3.4.1. We used Picard tools (http://broadinstitute.github.io/picard/) to deduplicate reads and HTseq to count reads with parameters stranded=yes and type=exon.
Genome_build: Synechocystis sp. PCC 6803
Supplementary_files_format_and_content: raw counts text files

molecule: total RNA

organism: Synechocystis sp. PCC 6803

source_name: cell suspension

growth_protocol: Cultures were grown in modified liquid blue-green (BG-11) medium (Andersen, 2005) buffered with 10 mM TES–KOH, pH 7.5 and bubbled with filtered (Millex®-FG, 50mm, PTFE 0.2 µm pore size, Merck KGaA, Darmstadt, Germany) CO2-enriched air (1% (v/v); BOC Industrial Gases, UK) at a rate of ~ 200 mL s-1. Cultures were grown under continuous illumination of 150 µmol photons m2 s-1 of cool white (6500K) light supplied by light emitting diodes (LED; The Optoelectronic Manufacturing Corporation (UK) Ltd., Cornwall, UK) that were evenly spaced around the culture vessel.

extract_protocol:
Tri-Reagent as per manufacturers instructions including a DNAse treatment step
TruSeq Stranded mRNA Sample Preparation, 1. Purify and fragment mRNA, 2. Synthesize First Strand cDNA, 3. Adenylate 3' ends, 4. Ligate Adapters, 5. Enrich DNA Fragments, 6. Pooling at with a pool average size of  336bp. The raw reads were pre-processed including the removal of low-quality bases and sequencing adapters (CGR, Liverpool).

treatment_protocol: See "overall design"

tag: control (c) or treatment (t)

value: C

tag: biological replicate

tag: time point


title: Sample T2 Cyto technical replicate c

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: PDAC Nucleolin Inhibitor Cytoplasm sample 1 technical replicate c

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.1. Before mapping, poly N read tail were trimmed, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from Ensembl version 88) using the STAR mapper (version 2.5.2b, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Mus musculus GTF genome annotation from Ensembl version 88. All overlapping regions between alignments and referenced exons were counted and aggregated by genes with HTSeq-count 0.5.3.
Genome_build: mm10 version Ensembl 88
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

organism: Mus musculus

source_name: PDAC

extract_protocol:
Trizol extraction
Messenger (polyA+) RNAs were purified from 300 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina)

treatment_protocol: mPDAC cells were treated for 48 hours with N6L

tag: genetic background

value: FVB/N x C57BL6

tag: age

tag: treatment

value: Nocleolin inhibitor

tag: cellular compartment

value: Cytoplasm


title: C2.9


title: C2.2


title: Sample T2 Cyto technical replicate b

description: PDAC Nucleolin Inhibitor Cytoplasm sample 1 technical replicate b


title: Sample T3 Cyto technical replicate d

description: PDAC Nucleolin Inhibitor Cytoplasm sample 3 technical replicate d


title: C2.7


title: C2.0


title: Sample T1 Cyto technical replicate c


title: wildtype_HCT116_wt_Ki67HPA_r1

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Ki67HPA.
pADamID_15

library_source: genomic

data_processing:
library strategy: pA-DamID
1. pA-DamID: the full protocol is described in the corresponding manuscript; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts; remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17; reads overlapping GATC fragments were counted in 50 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of the target protein over the Dam control using custom R scripts.
2. RNA-seq: the full protocol is described in the corresponding manuscript; adapter sequences and low quality reads were removed with fastp 0.12.2; reads were aligned to hg38 and counted in gencode v24 genes with STAR 2.5.4a; STAR was also used to create BigWig tracks of uniquely mapped reads; DESeq2 1.30.1 was used to call differentially expressed genes and compute FPKM values.
3. Repli-seq: adapter sequences and low quality reads were removed with fastp 0.12.2; reads were processed as described for pA-DamID, except that duplicated reads were removed and reads were not required to overlap with GATC fragments.
Genome_build: hg38
Supplementary_files_format_and_content: 1. pA-DamID: BigWig files of log2-normalized pADamID scores for 50 kb genomic bins, tsv files with genomic coordinates and all scores per replicate / average scores per condition (including previously published pA-DamID data used in this study), tsv file with complete metadata that includes target/Dam control combinations; 2. RNA-seq: BigWig files of read coverage, tsv file with read counts; 3. Repli-seq: BigWig tracks of quantile-normalized early/late log2-ratios.

molecule: genomic DNA

organism: Homo sapiens

source_name: HCT116 (ATCC CCL-247)

growth_protocol: hTERT-RPE, HCT116 and K562 cells (all from ATCC) were cultured according to their ATCC guidelines.

extract_protocol:
1. pA-DamID: 1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a primary antibody and for a Dam control condition, to specifically deposit m6A marks at chromatin nearby the primary antibody. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit; 2. RNA-seq: RNA was isolated using the Qiagen RNeasy column purification kit; 3. Repli-Seq: cells were harvested as for pA-DamID and immediately fixed in ice-cold ethanol.
1. pA-DamID: the full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at m6A-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified and further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; 2: RNA-seq: sequencing libraries were prepared using the Illumina TruSeq polyA stranded RNA kit; 3: replicated DNA was enriched for with a BrdU IP, before libraries were prepared as described in Marchal, 2018.

treatment_protocol: 1. Wildtype: no treatment; 2. Cell cycle: cells were synchronized with a sequential treatment of G2 enrichment (16 hours, with RO-3306) and metaphase blocking (90 minutes, with nocodazole). Synchronized cells were harvested with a mitotic shake-off, and immediately processed for pA-DamID or replated for interphase time points; 3. Ki67-AID: protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich, in DMSO, 24 h depletion), a similar amount of DMSO was used as control; 4. Actinomycin D: nucleoli were disrupted with a low dose of actinomycin D (50 ng/mL, in DMSO, 3 h treatment), a similar amount of DMSO was used as control; 5. Osmotic shock: nucleoli were disrupted with a short osmotic shock (0.2x PBS, 15 minutes), cells were harvested at two time points during nucleolar recovery; 6. Repli-seq: BrdU was added to a final concentration of 100 uM and cells were incubated at 37 °C for another 2 h.

tag: cell type

value: Colorectal carcinoma cells

tag: library type

value: pA-DamID

tag: experiment

value: wildtype

tag: condition

value: wt

tag: target


title: C12 KO + C. parvum 24h 3

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

country: USA

institute: creighton university

data_processing:
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Rmats  v3.2.5 with parameters  -analysis U -t paired -a 8.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts and FPKM values for each Sample

source_name: C12 KO + C. parvum 24h

extract_protocol:
cells were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104).  Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 platform

value: intestinal epithelial

tag: cell line

tag: genotype

value: IEC4.1-Ifnar1-/- KO

tag: agent

value: C. parvum


title: Sample T3 Cyto technical replicate b

description: PDAC Nucleolin Inhibitor Cytoplasm sample 3 technical replicate b


title: Sample T3 Cyto technical replicate c

description: PDAC Nucleolin Inhibitor Cytoplasm sample 3 technical replicate c


title: wildtype_K562_wt_Ki67_r1

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_19

value: Chronic myeloid leukemia cells


title: C2.5


title: wildtype_K562_wt_Ki67_r2

description:
pA-DamID on K562 (ATCC CCL-243) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_20


title: Sample T2 Cyto technical replicate d

description: PDAC Nucleolin Inhibitor Cytoplasm sample 1 technical replicate d


title: wildtype_HCT116_wt_Ki67NOV_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Ki67NOV.
pADamID_18


title: C12 KO + C. parvum 24h 2


title: Sample T1 Cyto technical replicate a

description: PDAC Nucleolin Inhibitor Cytoplasm sample 1 technical replicate a


title: wildtype_HCT116_wt_Ki67NOV_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Ki67NOV.
pADamID_17


title: Sample NT2 Poly technical replicate d

description: PDAC Control Polysom sample 2 technical replicate d

value: Control

value: Polysom


title: Sample T2 Cyto technical replicate a

description: PDAC Nucleolin Inhibitor Cytoplasm sample 2 technical replicate a


title: C2.4


title: Sample NT2 Poly technical replicate c

description: PDAC Control Polysom sample 2 technical replicate c


title: wildtype_HCT116_wt_Ki67_r3

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_11


title: C2.1


title: wildtype_HCT116_wt_Ki67HPA_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Ki67HPA.
pADamID_16


title: wildtype_HCT116_wt_H3K27me3_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: H3K27me3.
pADamID_13


title: Sample T1 Cyto technical replicate b

description: PDAC Nucleolin Inhibitor Cytoplasm sample 1 technical replicate b


title: wildtype_HCT116_wt_H3K27me3_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: H3K27me3.
pADamID_14


title: Sample T1 Cyto technical replicate d


title: wildtype_HCT116_wt_Ki67_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_9


title: wildtype_HCT116_wt_LMNB1_r1

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: LMNB1.
pADamID_12


title: wildtype_HCT116_wt_Ki67_r2

description:
pA-DamID on HCT116 (ATCC CCL-247) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_10


title: Sample NT2 Poly technical replicate b

description: PDAC Control Polysom sample 2 technical replicate b


title: C12 KO  control 3

source_name: C12 KO control


title: C12 KO  control 1

source_name: C12 KO  control


title: C12 KO + C. parvum 24h 1


title: IEC4.1 WT + C. parvum 24h 2

source_name: IEC4.1 WT + C. parvum 24h


title: C12 KO  control 2


title: wildtype_RPE_wt_H3K9me3_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: H3K9me3.
pADamID_7

source_name: hTERT-RPE (ATCC CRL-4000)

value: hTERT-immortalized retinal pigment epithelial cells


title: Sample NT2 Poly technical replicate a

description: PDAC Control Polysom sample 2 technical replicate a


title: wildtype_RPE_wt_H3K27me3_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: H3K27me3.
pADamID_6


title: wildtype_RPE_wt_H3K9me3_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: H3K9me3.
pADamID_8


title: wildtype_RPE_wt_H3K27me3_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: H3K27me3.
pADamID_5


title: IEC4.1 WT + C. parvum 24h 1


title: IEC4.1 WT + C. parvum 24h 3


title: IEC4.1 WT control 1

source_name: IEC4.1 WT control


title: Sample NT2 Cyto technical replicate d

description: PDAC Control Cytoplasm sample 2 technical replicate d


title: IEC4.1 WT control 2

source_name: IEC4.1 WT  control


title: Sample NT1 Poly technical replicate c

description: PDAC Control Polysom sample 1 technical replicate c


title: IEC4.1 WT control 3


title: Sample NT1 Poly technical replicate b

description: PDAC Control Polysom sample 1 technical replicate b


title: Sample NT2 Cyto technical replicate c

description: PDAC Control Cytoplasm sample 2 technical replicate c


title: Sample NT1 Poly technical replicate d

description: PDAC Control Polysom sample 1 technical replicate d


title: wildtype_RPE_wt_Ki67_r1

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_1


title: wildtype_RPE_wt_Ki67_r4

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_4


title: Sample NT1 Cyto technical replicate d

description: PDAC Control Cytoplasm sample 1 technical replicate d


title: wildtype_RPE_wt_Ki67_r2

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_2


title: day 3 con rep3

city: harbin

first: Qi

last: Jiang

state: heilongjiang

address: baojian road 157

department: Department of histology and embryology

country: China

institute: Harbin Medical University

data_processing:
HISAT v2.0.4 --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Mouse embryonic fibroblasts (MEFs) were obtained from 13.5-dpc embryos collected from homozygous 4F2A females or C57BL/6 females which had been mated with DBA/2 males. 293T and MEFs were cultured in Dulbecco's modified eagle medium (DMEM) containing 15%(vol/vol) fetal bovine serum (FBS), 1X MEM NEAA, 1X L-Glutamine and 1X Penicillin-Streptomycin. (FBS from BI and others from Invitrogen). For iPSC reprogramming, infected or drug treated 4F2A MEFs were cultured in KnockOut DMEM with 15% KnockOut Serum Replacement, 1X MEM NEAA, 1X L-Glutamine, 1X Penicillin-Streptomycin, 1X Sodium Pyruvate, 1000U/ml LIF, 1X 2-Mercaptoethanol and 2 μg/ml doxycycline (LIF from Millipore, doxycycline from Sigma-Aldrich and others from Invitrogen), the medium were changed every day.

extract_protocol:
48 hrs after infection or 72h post DOX was added, the total RNA of 4F2A MEFs was harvested by using TRIzol reagent (Invitrogen).Total RNA was extracted according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: strain

value: Mouse embryonic fibroblasts (MEFs)

tag: genotype/variation

value: control

tag: time

value: 5 days post infection


title: day 3 oe rep2

value: KDM6A overexpression


title: day 3 oe rep1


title: CD8+NRP-V7+ from the pancreas [panc_4]

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: pooled from 9 mice with hash-tagged oligos marking individual mice

data_processing:
VDJ and single-cell RNA-seq including hash-tagged oligos (HTO; used to label cells coming from the same mouse), and antibody-derived tags (ADT; used to label cells based on the expression of selected surface markers) data were processed with CellRanger. In brief, raw read files were processed and aligned using the CellRanger pipeline (cellranger-5.0.0 with refdata-gex-mm10-2020-A).
Read counts representing gene expression were used for removing barcodes representing empty droplets or droplets with high amounts of mitochondrially encoded gene products: using the isOutlier() function of the scater package, all cells whose fractions of mitochondrial reads were higher than 3x median absolute deviation (MAD) were flagged and removed as well as cells with fewer than 10^2.5 detected genes. Following the first round of filtering, HTO demultiplexing and doublet detection were done with CiteFuse, removing more droplets and identifying the donor mouse for each remaining droplet. After removal of low-quality droplets and barcodes associated with HTO-inferred doublets, ADT values were normalized using DropletUtils::inferAmbience() and scuttle::medianSizeFactors(). Finally, droplets for which less than 50% of the ADT were detected compared to other droplets were removed and only genes that were expressed in at least 5 cells per sample were kept for downstream analyses.
VDJ sequencing data was imported into R using the import_vdj() function of the djvdj package, which was adjusted to work with SingleCellExperiment objects (https://github.com/friedue/SCEdjvdj).
Size-factor normalized logcounts were obtained via scran::computeSumFactors() and scater::logNormCounts() (Lun et al, 2016; doi: 10.1186/s13059-016-0947-7, McCarthy et al., 2017, doi: 10.1093/bioinformatics/btw777). Cells from the three different technical replicates were integrated with batchelor::fastMNN() using the top 2500 most variable genes with min. mean normalized expression of 0.001 (Haghverdi et al., 2018, doi: 10.1038/nbt.4091). Clustering was performed with igraph::cluster_louvain(), dimensionality reductions were done with scater functions (runUMAP()) using the batch-corrected values and destiny::diffusionMap() (Lun et al., 2016, doi: 10.12688/f1000research, Angerer et al., 2016, doi: 10.1093/bioinformatics/btv715). The TSCAN package (v.1.28.0) was used to calculate pseudotime values and trajectories as well as genes associated with the pseudotime gradients (Ji & Ji, 2016, doi: 10.1093/nar/gkw430).
Genome_build: GRCm38 (provided by CellRanger (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)
Supplementary_files_format_and_content: Unfiltered CellRanger single-cell expression output (background and cell associated barcodes) entails tsv files for barcodes and features, and a count matrix (matrix.mtx). Each matrix is stored in the Market Exchange Format (MEX) for sparse matrices and contains  number of UMIs associated with a feature (row) and a barcode (column). Gzipped TSV files have feature and barcode sequences corresponding to row and column indices of the matrix, respectively. Output from CellRanger's Single Cell Immune Profiling: comma-separated high-level annotations on the assembled TCR contigs with one contig, consensus, or clonotype per row. More processed files incl the assignment of individual mice to TCR clonotypes can be found at https://github.com/abcwcm/GeartySchietinger/blob/master/scRNAseq/data/.
Supplementary_files_format_and_content: R object (SingleCellExperiment format) with counts and size-factor normalized logcounts fo 14546 genes and 5055 pLN cells; normalized log-transformed values for CITE-seq values are part of the colData as well as information about cluster identities and the T cell population (AIC = Tcf1-hi, stem-cell like; AMC = Tcf1-lo/CD62L-lo effector cells) and pseudotime values. For more details see https://github.com/abcwcm/GeartySchietinger
Supplementary_files_format_and_content: tcr_perCell_pairedSamples_newCID_2021-05.rds: Robject of type data.table/data.frame with clonotype IDs, cell barcodes and labels for cells that were found in the VDJ sequencing of pLN as well as pancreas samples from the same mouse. For more details see https://github.com/abcwcm/GeartySchietinger/blob/master/scRNAseq/processingVDJseq.md. All processing scripts have also been registered with zenodo: https://zenodo.org/record/5525867

source_name: CD8+ T lymphocyte

extract_protocol:
NRP-V7+ CD8+ T cells were isolated from the pancreatic lymph node or pancreas via FACS and sorted into PBS + 0.04% BSA for analysis of cell count and viability.
Single-cell RNA-Seq (chemistry: Single Cell 5' R2-only: Sorted cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 1,700-6,500 cells proceeded using the Chromium Single Cell 5’ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 14-18 cycles and 9-48ng of the material were used to prepare sequencing libraries with 14-16 cycles of PCR. Indexed libraries were pooled by molarity and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 S1 Reagent Kit (100 cycles) (Illumina). An average of 97 million paired reads was generated per sample.
Single-cell V(D)J analysis from RNA: An aliquot of cDNA generated using the methods described above was used to enrich for V(D)J regions using the Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell (10X Genomics PN 1000071) according to the manufacturer’s protocol with 10 cycles of PCR during enrichment and 9 cycles during library preparation. Indexed libraries were pooled by molarity and sequenced on a NovaSeq 6000 in a PE150 run using the NovaSeq 6000 S4 Reagent Kit (300 cycles) (Illumina). An average of 24 million paired reads was generated per sample.
Cell surface protein feature barcode analysis: Amplification products generated using the methods described above included both cDNA and feature barcodes tagged with cell barcodes and unique molecular identifiers. Smaller feature barcode fragments were separated from longer amplified cDNA using a 0.6X cleanup using aMPure XP beads (Beckman Coulter catalog # A63882).  Libraries were constructed using the Chromium Single Cell 5’ Feature Barcode Library Kit (10X Genomics PN 1000080) according to the manufacturer’s protocol with 9 cycles of PCR. Indexed libraries were pooled by molarity and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 SP, S1, or S2 Reagent Kit (100 cycles) (Illumina). An average of 23 million paired reads was generated per sample.

value: NOD/ShiLtJ

tag: tissue

value: pancreas

value: CD8+ T lymphocyte


title: Sample NT2 Cyto technical replicate a

description: PDAC Control Cytoplasm sample 2 technical replicate a

value: FVB/N x C57BL6

value: Cytoplasm


title: wildtype_RPE_wt_Ki67_r3

description:
pA-DamID on hTERT-RPE (ATCC CRL-4000) cells; experiment: wildtype; condition: wt; target: Ki67.
pADamID_3

value: pA-DamID

value: wildtype

value: wt


title: Sample NT1 Poly technical replicate a

description: PDAC Control Polysom sample 1 technical replicate a


title: Sample NT2 Cyto technical replicate b

description: PDAC Control Cytoplasm sample 2 technical replicate b


title: day 3 con rep2


title: CD8+NRP-V7+ from the pancreas [panc_1]

description: pooled from 6 mice with hash-tagged oligos marking individual mice and antibody-derived tags against different proteins


title: day 3 oe rep3


title: CD8+NRP-V7+ from the pancreas [panc_3]

description: pooled from 10 mice with hash-tagged oligos marking individual mice

value: 16 weeks


title: pancreatic lymphnode CD8+NRP-V7+ [pLN_4]

description: pooled from 9 mice with hash-tagged oligos marking individual mice and antibody-derived tags against different proteins

molecule: polyA RNA

value: pancreatic lymph node


title: day 0 oe rep3

value: 2 days post infection


title: CRISP pooled library

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: CRISP pooled library

data_processing:
raw .fastq file was parsed to obtain sgRNA abundance values using regular expression (stagger+BARCODE)(primer)(sgRNA), where stagger+BARCODE sequences were (atAAGTAGAG|gatAAGTAGAG) corresponding to PDL1 and control samples correspondingly, primer sequence TCTTGTGGAAAGGACGAAACACCG  and sgRNA sequence of 20bp length from the Epigenetic sgRNA library
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each sgRNA from the libarary

source_name: ID8 cell line

extract_protocol:
Genomic DNA was extracted using salt precipitation. In brief, cell pellets (1-5 X 107 cells) were suspended in 6 ml gDNA lysis buffer (50 mM EDTA, 1% SDS, 50 mM Tris pH 8.0) and added 30 l 20 mg/ml proteinase K (Fisher Scientific, #25-530-049) at 55 °C overnight. And then 30 l 10 mg/ml RNase A (Thermo Fisher, #EN0531) was added and incubated at 37 °C for 30 min, then cooled on ice. Protein was precipitated by adding 2 ml 7.5 M stock solution of Ammonium Acetate and centrifuging at > 4000 g for 10 min. The supernatant containing genomic DNA was collected and precipitated by adding 6 ml 100% isopropanol and centrifuging at > 4000 g for 10 min. DNA pellet was washed with 70% ethanol, air dried and dissolved in H2O for PCR amplification.
Library was constructed by a two-step PCR amplification. The first PCR was performed in 8 PCR reactions each containing 5 g gDNA, 1.5 l 10 M forward and reverse primers, 50 l NEBNext Q5 HotStart HiFi PCR Mastermix for 15 cycles of 98 °C, 20 s; 60 °C, 30 s; 65 °C, 45°C. The first PCR product from the same sample was pooled together and purified by AMPure XP beads (Beckman Coulter) following the manufacturer’s instructions and suspended in 800 l H2O. To barcode the samples, for each sample, three second PCR reactions containing 10 l first PCR product, 1l 10 M forward and reverse Illumina primers, 50 l NEBNext Q5 HotStart HiFi PCR Mastermix for 20 cycles of 98 °C, 20 s; 60 °C, 30 s; 65 °C, 45°C. The final PCR product was purified by AMPure XP beads (Beckman Coulter) following the manufacturer’s instructions

tag: stagger

value: at/gat

tag: barcode

value: AAGTAGAG


title: pancreatic lymphnode CD8+NRP-V7+ [pLN_1]

description: pooled cells from 10 mice with hash-tagged oligos marking individual mice and antibody-derived tags against different proteins

tag: age

value: 13-19 weeks


title: Klf5 Knockdown E4.5 Embryo replicate 6

city: Berkeley

first: Martin

last: Kinisu

state: California

address: 300C Li Ka Shing Building

department: MCB

institute: University of California Berkely

data_processing:
Gene expression levels are quantified by Kallisto v0.46 with kallisto -quant and default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Text file for matrix of expression levels of genes, with first column is the gene name, and the first row is the sample ID.

source_name: E4.5  embryos

growth_protocol: Embryos were cultured in KSOM supplemented with BSA (1mg/ml) under a layer of parafin oil at 37C 5% CO2 and normoxia

extract_protocol:
RNA extraction and cDNA synthesis was performed using SMARTseq-V4 kit. cDNA was then purified with AMPure XP beads
RNA-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645), diluting NEB adaptors 1:5 and performing 8 PCR cycles.

value: Preimplantation embryos harvested from C57BL/5J mice

value: E4.5 Mouse embryos treated with Klf5 siRNA


title: pancreatic lymphnode CD8+NRP-V7+ [pLN_3]

description: pooled from 10 mice with hash-tagged oligos marking individual mice and antibody-derived tags against different proteins


title: Klf5 Knockdown E4.5 Embryo replicate 4


title: day 0 oe rep1

value: Mouse embryonic fibroblasts (MEFs)

value: KDM6A overexpression


title: SETDB1 KO cells, sgRNA 2, replicate 3

description: SETDB1 KO cells, sgRNA 2, replicate 3

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

extract_protocol:
Total RNA of control ID8 and two Setdb1 knockout ID8 cell lines was extracted using RNeasy mini Kit (Qiagen, #74106) and digested with DNase I (Qiagen, #79254).
RNA-seq libraries were constructed using ScriptSeq complete Gold kit (Epicentre, #SCL24EP)

value: KO

tag: sgrna

tag: replicate


title: day 3 con rep1

tag: cell type

value: control

value: 5 days post infection


title: day 0 con rep2


title: Klf5 Knockdown E4.5 Embryo replicate 2


title: Klf5 Knockdown E4.5 Embryo replicate 3


title: SETDB1 KO cells, sgRNA 2, replicate 2

description: SETDB1 KO cells, sgRNA 2, replicate 2


title: SETDB1 KO cells, sgRNA 2, replicate 1

description: SETDB1 KO cells, sgRNA 2, replicate 1


title: 24. Sc12+Trp+IB

city: Taipei

first: Hsien-Lin

last: Liu

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

data_processing:
Basecalling: Illumina Real-Time Analysis Software. Fastq: bcl2fastq version 2.18.
Data Trimming Process and Quality check: Trimmomatic (v0.39) and FastQC (No trimming was made except the make-up datas. The one-end of make-up data reads (paired-end) was selected for trimming as long as other samples (single-end) and applied for further analysis.)
Alignment to S. cerevisiae S288c genome (UCSC sacCer3) by TopHat (2.1.1)/Bowtie2.
Cufflinks-2.2.1.Linux_x86_64 was used to calculate fragments per kilobase of transcript per million (FPKM) values and differentially expressed genes (DEGs) with the criteria of |Log2(Fold change)|>1 and q-value< 0.05.
Genome_build: Download reference genome: S. cerevisiae S288c genome (UCSC sacCer3).
Supplementary_files_format_and_content: FPKM_of_each_replicate.xlsx: Excel file includes fragments numbers and FPKM values for each sample.
Supplementary_files_format_and_content: Differential_expression_tests_genes.xlsx: Excel file includes log2(fold_change) and q-value for each sample pair.

organism: Saccharomyces cerevisiae S288C

source_name: TRP5 defected strain

growth_protocol: The yeast was cultured in 4ml YPD (yeast extract 10 g/L, peptone 20 g/L, and glucose 20 g/L) at start OD600nm 0.5.

extract_protocol:
After 24 hours, cells were harvested for total RNA extraction using QIAGEN RNeasy® Mini kit (Qiagen, Germany).
RNA Library was prepared by SuperScript™ III Reverse Transcriptase (Thermo Fisher) and TruSeq RNA LT kits (Illumina, USA) for fragment size around 350 to 500 bps.

treatment_protocol: The sample was treated with/without 1.2% Isobutanol and/or Trp 200ug/ml for assay in three replicates.

value: Tryptophan synthase (TRP5) defective

tag: tryptophan addition

value: Yes

tag: isobutanol addition


title: Klf5 Knockdown E4.5 Embryo replicate 5


title: day 0 oe rep2


title: Control E4.5 Embryo replicate 10

value: E4.5 Mouse embryos treated with scramble siRNA


title: day 0 con rep3


title: SETDB1 KO cells, sgRNA 1, replicate 2

description: SETDB1 KO cells, sgRNA 1, replicate 2


title: 22. Sc12+Trp+IB


title: SETDB1 WT cells, replicate 3

description: SETDB1 WT cells, replicate 3

value: WT


title: SETDB1 KO cells, sgRNA 1, replicate 1

description: SETDB1 KO cells, sgRNA 1, replicate 1


title: Sample NT1 Cyto technical replicate b

description: PDAC Control Cytoplasm sample 1 technical replicate b

tag: genetic background

value: FVB/N x C57BL6

tag: treatment

value: Control

tag: cellular compartment

value: Cytoplasm


title: 21. Sc12+IB

tag: genotype

value: No


title: Sample NT1 Cyto technical replicate c

description: PDAC Control Cytoplasm sample 1 technical replicate c


title: SETDB1 WT cells, replicate 1

description: SETDB1 WT cells, replicate 1


title: Klf5 Knockdown E4.5 Embryo replicate 1

tag: cell line


title: Sample NT1 Cyto technical replicate a

description: PDAC Control Cytoplasm sample 1 technical replicate a


title: 23. Sc12+Trp+IB


title: Control E4.5 Embryo replicate 4


title: Control E4.5 Embryo replicate 8


title: day 0 con rep1

tag: strain

value: 2 days post infection


title: SETDB1 KO cells, sgRNA 1, replicate 3

description: SETDB1 KO cells, sgRNA 1, replicate 3


title: Control E4.5 Embryo replicate 6


title: 15. Sc12

description:
Make-up data
FPKM_of_each_replicate.xlsx


title: Control E4.5 Embryo replicate 1


title: Control E4.5 Embryo replicate 2


title: SETDB1 WT cells, replicate 2

description: SETDB1 WT cells, replicate 2


title: 18. Sc12+Trp


title: 16. Sc12+Trp


title: 17. Sc12+Trp


title: 20. Sc12+IB


title: 508_LN

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

data_processing:
Mapping with STAR_2.4.0a versus mm10 folowing Encode RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20".  Raw count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M -C" options.
Raw count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M -C" options.
RNAseq data were quantified using RSEM sofware 1.2.25 (Li and Dewey, 2011) with bowtie2-2.2.6 and m38 as reference genome.
Genome_build: mm10

source_name: Lymph node

extract_protocol:
Total RNA was extracted from splenocytes of tumor developing plck-GAPDH mice and wt mice using the RNA extraction kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions.
Truseq Stranded Total RNA
Libraries were generated from 500ng of total RNAs using Truseq Stranded Total RNA kit (Illumina). Libraries were then quantified with Qubit and pooled. 4nM of this pool were loaded on a High Output Flowcell and sequenced on a NextSeq500 platform (Illumina) with 2x75bp paired-end chemistry.

value: Lymph node

value: plckGAPDH

value: > 18 months


title: Control E4.5 Embryo replicate 9

value: Preimplantation embryos harvested from C57BL/5J mice


title: Control E4.5 Embryo replicate 5


title: Control E4.5 Embryo replicate 3


title: 12. WT+Trp+IB

source_name: Wild type


title: 19. Sc12+IB


title: Control E4.5 Embryo replicate 7


title: 343_rateA

source_name: Spleen

value: Spleen


title: 547_rateA


title: Snubar-mouse3

city: Houston

first: Anil

middle: K

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

description:
Snubar-mouse3_ATAC and Snubar-mouse3_BC
SnubarATAC-mouse-drug-treatment-3-scATAC and sample_barcode
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger atac V1.2.0 mkfastq
cellranger atac V1.2.0 count and cellranger-arc-1.0.0 count
Mixing experiment data was aligned to the combined reference genomes of human (hg19 reference) and mouse (mm10 reference). All other experimental data was aligned to human hg19 or mouse mm10 genome.
UMI counts and peak count are summarized
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI and Peak values for each Sample

growth_protocol: The A20 and K562 cell lines were purchased from the American Type Culture Collection and cultured based on ATCC guidelines. The MDA-MB-231 and MDA-MB-436  cell lines were obtained from the MD Anderson Characterized Cell Line Core Facility and were cultured in Dulbecco’s Modified Eagle’s Medium-high glucose medium supplemented with 10% FBS  and 1X penicillin-streptomycin. Mice were purchased from the Jackson Laboratory and housed in the Research Animal Support Facility at MD Anderson Cancer Center.

extract_protocol:
Cell nuclei for Snubar-ATAC were isolated according to Nuclei Isolation for Single Cell ATAC Sequencing Protocol (CG000169 Rev D, 10X Genomics) or Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing Protocol (CG000212 Rev B, 10X Genomics). Nuclei used for SNubar-ARC were isolated according to Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol (10X Genomics, CG000365 Rev A).
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics protocols (CG000168 Rev A for Chromium Single Cell ATAC Reagent Kits,  CG000209 Rev D for Chromium Next GEM Single Cell ATAC Library Kit v1.1, or CG000338 Rev A for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression)
single cell ATAC-seq, single cell RNA&ATAC co-assay, and barcode libraries

treatment_protocol: 28 mice were treated under 7 different conditions (4 mice in each group): 1) Control; 2) Chemotherapy + 2 Gy Radiotherapy; 3) 4 Gy Radiotherapy; 4) Chemotherapy + 2 Gy Radiotherapy + Talazoparib; 5) Chemotherapy + 2 Gy Radiotherapy + PD-L1 Blockade; 6) 4Gy Radiotherapy + PD-L1 Blockade; 7) 4Gy Radiotherapy + Talazoparib + PD-L1 Blockade.

value: syngeneic lung tumors derived from LKR13 lung cancer cell line


title: 10. WT+Trp+IB


title: Control, replicate 1

source_name: embryonic stem cells

growth_protocol: Mouse ESCs were cultured using Knockout DMEM supplemented with NEAA (0.1mM), BME(0.1mM), L-Glutamine (1mM), pen/strep (1x) and LIF (1000u/ml) on irradiated MEF feeders derived from C57BL/6J mice at E13.8 at 37C and 5% CO1

extract_protocol:
Total RNA was extracted by Direct-zol RNA extraction Kit by Zymo Research. mRNA (polyA) purification, RNA fragmentation, first and second strand cDNA synthesis were performed according to the TruSeq RNA Sample Preparation v2 Kit using Superscript III for reverse transcription (50-min incubation at 50 degrees celsius). cDNA was purified with AMPure XP beads diluted 1:2 with 20% PEG, 1.25M NaCl, and eluted in 27.5 μl of 10 mM Tris-HCl pH 7.9, 25 μl of which were transferred to a new tube and subjected to library construction.
RNA-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645), diluting NEB adaptors 1:5 and performing 8 PCR cycles.

value: Mouse embryonic stem cells derived from C57BL/6J mice

value: Mouse embryonic stem cells overexpressing GFP


title: WT1

value: Wild type


title: 331_rate


title: 455_MES


title: Klf5 OE, replicate 2

growth_protocol: Mouse ESCs were cultured using Knockout DMEM supplemented with NEAA (0.1mM), BME(0.1mM), L-Glutamine (1mM), pen/strep (1x) and LIF (1000u/ml) on irradiated MEF feeders derived from C57BL/6J mice at E13.8 at 37C and 5% CO2

value: Mouse embryonic stem cells overexpressing Klf5


title: WT4


title: 13. Sc12

value: Tryptophan synthase (TRP5) defective


title: 14. Sc12


title: V3C_u2os_raav_24hpi_2

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

data_processing:
Reads were aligned to the human hg38 genome using Bowtie2.
Aligned V3C-seq samples were sorted using Samtools, and the resulting aligned and sorted Bam files were converted to Bedgraph files using Bedtools.
ChIP-seq peaks were called using the SICER algorithm on EPIC software platform.
Biological replicates of the samples were determined using Bedtools.
Genome_build: Human hg38
Supplementary_files_format_and_content: bed files from peak calling using EPIC or bdgraph (rpm calculated)

source_name: Epithelial

growth_protocol: Prental human U2OS and HEK-293FT cells as well as stable U2OS and HEK-293T cells expressing Rep68/78 upon induction with doxcycline were propagated in 5% Serum Plus (Sigma Aldrich) containing DMEM media (Gibco) supplemented with Gentamicin at 37oC and 5% carbon dioxide. AAV2 and rAAV infections were carried out a Multiplicity of Infection (MOI) of 5000 and cells were harvested at the indicated time points [(24 or 36 hours post infection (hpi)]. Samples were processed for Chromatin mmunoprecipitation (ChIP-seq) or Chromosome Conformation Capture (V3C-seq) assays.

extract_protocol:
For ChIP assays, lysates were clarified from sonicated nuclei (Diagenode), and DNA-protein complexes were immunoprecipitated using antibodies conjugated to Dynabeads (ThermoScientific). For Viral Chromosome Conformation Capture assays, AAV2/rAAV infected cells were crosslinked in 2 percent formaldehyde for 10 minutes, quenched in 0.125 M glycine for 5 minutes, collected and lysed in NP-40 containing 3C Lysis buffer for 10 minutes before being subjected to primary restriction enzyme digestion overnight with 400 U of HindIII. Following digestion, the restriction enzyme was inactivated and samples were subjected to intramolecular ligation with T4 DNA Ligase at room temperature. Samples were then reverse crosslinked and purified, before digesting in the secondary restriction enzyme, NlaIII. NlaIII was heat inactivated, samples were purified by phenol:chloroform purification, and circularized using T4 DNA Ligase. Samples were purified using a PCR Purification Kit (Qiagen), and equivalent amounts of DNA was used to perform inverse PCR with primers complementary to the AAV2/rAAV genome. Inverse PCR samples were diluted 1:100 in TE, before being used as templates for nested-inverse PCR reactions. 6 independent nested-inverse PCR reactions were pooled, PCR purified using a Qiagen kit and submitted for library preparation and high-throughput sequencing.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (cat # E7645L) according to manufacturer's instructions. Twelve samples were pooled per run and samples were analyzed by 75 bp single-end sequencing on the NextSeq 500 (Illumina).

treatment_protocol: For ChIP-seq experiments, stable U2OS and 293T Rep-expessing cell lines were induced with 500 ng/ml Doxycycline hydrochloride (MP Biomedicals) for 24 hours and when indicated cells were treated with 1 mM Hydroxyurea (Sigma Aldrich) at 12 hours post induction for 12 hours. When indicated, HEK-293FT cells were transfected with 1 μg pHelper plasmid 24 hours prior to AAV2 infection.

tag: disease

value: Osteosarcoma

value: Bone

value: Epithelial


title: 508_rate


title: 4. WT+Trp

value: WT

value: Yes


title: 5. WT+Trp

value: No


title: 7. WT+IB


title: V3C_u2os_raav_24hpi_1


title: Klf5 OE, replicate 1


title: 11. WT+Trp+IB


title: V3C_293_raav_24hpi_2

value: Kidney


title: 3. WT


title: WT5


title: 8. WT+IB


title: 9. WT+IB


title: V3C_u2os_aav_24hpi_2


title: 6. WT+Trp


title: Naïve CD4 T cell rep2

city: CLAYTON

first: Aidil

last: Zaini

state: VICTORIA

address: LEVEL 3, BUILDING 77, MONASH UNIVERSITY

department: BIOCHEMISTRY AND MOLECULAR BIOLOGY

country: Australia

institute: MONASH UNIVERSITY

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al., 2013) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GRCm38 was used
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts, text file, tab separated

source_name: mesenteric lymph node

extract_protocol:
RNA from FACS-sorted cells was extracted using Rneasy Plus Micro Kit (QIAGEN) as per manufacturers’ standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were infected with either low dose/LD/30 or high dose/HD/200 parasitic eggs and culled 21 days after infection, and mesentric lymph nodes were extracted. Tfh cells (CD4+ CD44hi FOXP3- Ly6C- CD162- PD-1+ CXCR5+) at d21 pi and naive Th cells (CD4+ FOXP3- CD44low CD62Lhigh ) from uninfected mice were FACS-sorted and purified for RNA extraction.

value: FIR mice

value: mesenteric lymph node

tag: post infection

value: not infected


title: V3C_293_aav_phelp_24hpi_2

tag: tissue


title: HD Tfh cell rep2

value: 21 days


title: V3C_293_aav_24hpi_2


title: V3C_293_raav_24hpi_1


title: AAD_78 [nasal]

type: RNA

city: Helsinki

first: Piia

last: Karisola

state: Southern Finland

address: Haartmaninkatu 3

department: Medical Faculty, Human Microbes Research Program Unit

country: Finland

institute: University of Helsinki

description:
SYM078
Study subject 78 belonging to the AAD group.

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into eUtopia bioinformatics package and analyzed with BioConductor package Limma. Data was quantile normalized based on cutoff 0.75 and percentage of samples 75%. Replicate control probes were combined by their median values.

source_name: Nasal biopsy

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: No cell culturing was involved.

extract_protocol: Total RNA was isolated from biopsies by RNeasy Plus Mini Kit (Qiagen). Quantity and quality of the samples were determined by NanoDrop spectrophotometer and Agilent Bioanalyzer 2100, respectively. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.

treatment_protocol: Nasal biopsies were mechanically disrupted by Ultra-turrax homogenizer.

tag: diagnosis

value: adult-onset asthma

tag: gender

value: Female

value: Nasal biopsy

tag: subject


title: Ctrl_623 [nasal]

description:
SAK623
Study subject 623 belonging to the Ctrl group.

value: healthy

tag: age


title: IEI_32 [nasal]

description:
SYM032
Study subject 32 belonging to the IEI group.

value: IEI


title: HD Tfh cell rep1


title: Ctrl_625 [nasal]

description:
SAK625
Study subject 625 belonging to the Ctrl group.


title: Control, replicate 2

growth_protocol: Mouse ESCs were cultured using Knockout DMEM supplemented with NEAA (0.1mM), BME(0.1mM), L-Glutamine (1mM), pen/strep (1x) and LIF (1000u/ml) on irradiated MEF feeders derived from C57BL/6J mice at E13.8 at 37C and 5% CO0

value: Mouse embryonic stem cells derived from C57BL/6J mice

value: Mouse embryonic stem cells overexpressing GFP


title: V3C_293_aav_24hpi_1


title: V3C_u2os_aav_24hpi_1

value: Osteosarcoma

value: Bone


title: 1. WT

value: WT

tag: replicate


title: Ctrl_639 [nasal]

description:
SAK639
Study subject 639 belonging to the Ctrl group.


title: Ctrl_620 [nasal]

description:
SAK620
Study subject 620 belonging to the Ctrl group.


title: V3C_293_aav_phelp_24hpi_1

tag: cell type

value: Epithelial


title: 2. WT

tag: tryptophan addition

value: No


title: APD_53 [nasal]

description:
SYM053
Study subject 53 belonging to the APD group.


title: PDL2.HI1

first: Adam

last: Mor

state: New York

address: 650 West 168 Street

institute: Columbia University

description: Human CD4 Cells

data_processing:
Expression count (STAR) analysis performed using BasePair software
Differential expression (DESeq2, compare 2 groups) performed using BasePair software. PDL1 Proliferating Donors 1 & 2 on PDL1 Non-Proliferating Donors 1 & 2
Differential expression (DESeq2, compare 2 groups) performed using BasePair software. PDL2 Proliferating Donors 1 & 2 on PDL2 Non-Proliferating Donors 1 & 2
Differential expression (DESeq2, compare 2 groups) performed using BasePair software. PDL1 Proliferating Donors 1 & 2 on PDL2 Proliferating Donors 1 & 2
Differential expression (DESeq2, compare 2 groups) performed using BasePair software. PDL1 Non-Proliferating Donors 1 & 2 on PDL2 Non-Proliferating Donors 1 & 2
Genome_build: hg19
Supplementary_files_format_and_content: Read counts by transcript

source_name: Non-Proliferating, Donor 3

growth_protocol: CD4 positive cells were isolated by positive selection from peripheral blood. Cells were then rested in RPMI-1640 supplemented with 10% heat inactivated FBS, 1% penicillin-streptomycin, 1X non-essential amino acids, 1mM sodium pyruvate, and IL-2 40 IU/mL for 72 hours.

extract_protocol:
Cells were sorted by CFSE fluorescence into RNA extraction buffer. RNA isolation was performed with the RNeasy Plus Mini Kit (Qiagen).
Illumina ultra-low input RNA

treatment_protocol: Rested cells were stained with 1 µM carboxyfluorescein succinimidyl ester (CFSE). Stained cells were then treated with anti-CD28 (1µg/mL) and added to 48 well plates coated with anti-CD3 (5µg/mL) and either PDL1 or PDL2 (5µg/mL).

value: peripheral blood derived CD4 cells

value: anti-CD3, anti-CD28, PDL2


title: APD_17 [nasal]

description:
SYM017
Study subject 17 belonging to the APD group.


title: U2OS_rAAV_24hpi_gh2ax_2

tag: chip antibody

value: Millipore #05-636 (5 ug)


title: AND_86 [nasal]

description:
SYM086
Study subject 86 belonging to the AND group.


title: AND_85 [nasal]

description:
SYM085
Study subject 85 belonging to the AND group.


title: Ki67_aid_HCT116_IAA_RNAseq_r3

description:
RNA-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA
RNA_6

data_processing:
1. pA-DamID: the full protocol is described in the corresponding manuscript; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts; remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17; reads overlapping GATC fragments were counted in 50 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of the target protein over the Dam control using custom R scripts.
2. RNA-seq: the full protocol is described in the corresponding manuscript; adapter sequences and low quality reads were removed with fastp 0.12.2; reads were aligned to hg38 and counted in gencode v24 genes with STAR 2.5.4a; STAR was also used to create BigWig tracks of uniquely mapped reads; DESeq2 1.30.1 was used to call differentially expressed genes and compute FPKM values.
3. Repli-seq: adapter sequences and low quality reads were removed with fastp 0.12.2; reads were processed as described for pA-DamID, except that duplicated reads were removed and reads were not required to overlap with GATC fragments.
Genome_build: hg38
Supplementary_files_format_and_content: 1. pA-DamID: BigWig files of log2-normalized pADamID scores for 50 kb genomic bins, tsv files with genomic coordinates and all scores per replicate / average scores per condition (including previously published pA-DamID data used in this study), tsv file with complete metadata that includes target/Dam control combinations; 2. RNA-seq: BigWig files of read coverage, tsv file with read counts; 3. Repli-seq: BigWig tracks of quantile-normalized early/late log2-ratios.

source_name: HCT116 (ATCC CCL-247)

value: Colorectal carcinoma cells

tag: genetic modification

value: OsTir1; Ki67-miniAID-mClover

tag: experiment

tag: condition


title: PDL2.HI3

description: Human CD4 Cells

source_name: Non-Proliferating, Donor 2

tag: treatment


title: Ki67_aid_HCT116_DMSO_RNAseq_r3

description:
RNA-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control
RNA_5

value: control


title: AAD_62 [nasal]

description:
SYM062
Study subject 62 belonging to the AAD group.

value: adult-onset asthma

value: Female


title: APD_33 [nasal]

description:
SYM033
Study subject 33 belonging to the APD group.

value: Nasal biopsy


title: U2OS_rAAV_24hpi_input


title: U2OS_rAAV_24hpi_gh2ax_1


title: PDL2.LO2

description: Human CD4 Cells

source_name: Proliferating, Donor 1


title: 293_aav_input

value: Kidney


title: Naïve CD4 T cell rep1

value: FIR mice

value: mesenteric lymph node

value: not infected


title: PDL2.LO1

description: Human CD4 Cells

source_name: Proliferating, Donor 3


title: PDL1.HI1

description: Human CD4 Cells

value: anti-CD3, anti-CD28, PDL1


title: 293_mock_input


title: AND_57 [nasal]

description:
SYM057
Study subject 57 belonging to the AND group.


title: 293_mock_gh2ax_2


title: PDL1.LO1

description: Human CD4 Cells


title: IEI_23 [nasal]

description:
SYM023
Study subject 23 belonging to the IEI group.

value: IEI


title: AND_84 [nasal]

description:
SYM084
Study subject 84 belonging to the AND group.


title: IEI_7 [nasal]

description:
SYM007
Study subject 7 belonging to the IEI group.


title: AND_80 [nasal]

description:
SYM080
Study subject 80 belonging to the AND group.


title: 293_pHelp_AAV_24hpi_gh2ax_1

value: Epithelial


title: Ki67_aid_HCT116_IAA_RNAseq_r1

description:
RNA-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA
RNA_2


title: APD_27 [nasal]

description:
SYM027
Study subject 27 belonging to the APD group.


title: PDL2.HI2

description: Human CD4 Cells

source_name: Non-Proliferating, Donor 1


title: Ki67_aid_HCT116_DMSO_RNAseq_r2

description:
RNA-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control
RNA_3


title: PDL1.HI2

description: Human CD4 Cells


title: Ki67_aid_HCT116_IAA_RNAseq_r2

description:
RNA-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA
RNA_4


title: 293_AAV_24hpi_gh2ax_2


title: 293_mock_gh2ax_1


title: PDL2.LO3

description: Human CD4 Cells

source_name: Proliferating, Donor 2


title: 293_pHelp_AAV_24hpi_gh2ax_2


title: Ctrl_643 [nasal]

description:
SAK643
Study subject 643 belonging to the Ctrl group.

value: healthy


title: Ki67_aid_HCT116_DMSO_RNAseq_r1

description:
RNA-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control
RNA_1


title: CTCF-AID-2d-2CLC-RNA-seq-rep2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
RNA-seq data analysis. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) with TopHat (version 2.1.1) with default parameters. All unmapped reads and non-uniquely mapped reads were removed. Gene counts were generated using HTSeq-count (version 0.9.1). For each sample, the gene count matrices were merged together and then the ‘Trimmed Mean of M values’ normalization (TMM) method from the R/Bioconductor package edgeR package (version 3.5.0) was used to calculate the normalized expression.
mm9
txt

source_name: mouse embryonic stem cells

growth_protocol:
mESCs were cultured routinely in LIF and serum medium.
mESCs were cultured routinely in LIF and serum medium.

extract_protocol: After FACS sorting in DPBS, mESCs were incubated in lysis buffer.  RNA-seq libraries were prepared using Smart-seq2 developed by Picelli et al., Nat Protoc 2014 (PMID: 24385147).

treatment_protocol: mESCs containing two stably integrated transgenes (MERVL::tdTomato; CTCF::AID) were cultured on 0.1% gelatin in DMEM containing 15% FBS, leukemia inhibiting factor (LIF), penicillin/streptomycin, L-glutamine, β-mercaptoethanol, and non-essential amino acids. After treatment with auxin for 2 days, ESCs (non-2CLCs) and 2CLCs were sorted using the fluorescent reporters. The cells were then lysed for Smart-seq2.

value: 129/Ola, XY

tag: transgene


title: Ki67_aid_HCT116_IAA_Repliseq_late_r2

description:
Repli-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA; target: late.
Repliseq_8

data_processing:
library strategy: Repli-seq
1. pA-DamID: the full protocol is described in the corresponding manuscript; the constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts; remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17; reads overlapping GATC fragments were counted in 50 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of the target protein over the Dam control using custom R scripts.
2. RNA-seq: the full protocol is described in the corresponding manuscript; adapter sequences and low quality reads were removed with fastp 0.12.2; reads were aligned to hg38 and counted in gencode v24 genes with STAR 2.5.4a; STAR was also used to create BigWig tracks of uniquely mapped reads; DESeq2 1.30.1 was used to call differentially expressed genes and compute FPKM values.
3. Repli-seq: adapter sequences and low quality reads were removed with fastp 0.12.2; reads were processed as described for pA-DamID, except that duplicated reads were removed and reads were not required to overlap with GATC fragments.
Genome_build: hg38
Supplementary_files_format_and_content: 1. pA-DamID: BigWig files of log2-normalized pADamID scores for 50 kb genomic bins, tsv files with genomic coordinates and all scores per replicate / average scores per condition (including previously published pA-DamID data used in this study), tsv file with complete metadata that includes target/Dam control combinations; 2. RNA-seq: BigWig files of read coverage, tsv file with read counts; 3. Repli-seq: BigWig tracks of quantile-normalized early/late log2-ratios.

tag: library type

value: Repli-seq

tag: target

value: late


title: Ki67_aid_HCT116_Repliseq_early_r2

description:
Repli-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control; target: early.
Repliseq_5

value: Colorectal carcinoma cells

value: early


title: CTCF-AID-2d-2CLC-RNA-seq-rep1

tag: strain


title: 293_AAV_24hpi_gh2ax_1

tag: tissue

value: Millipore #05-636 (5 ug)


title: APD_15 [nasal]

description:
SYM015
Study subject 15 belonging to the APD group.

tag: diagnosis

value: adult-onset asthma


title: Ki67_aid_HCT116_IAA_Repliseq_early_r2

description:
Repli-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA; target: early.
Repliseq_7

value: OsTir1; Ki67-miniAID-mClover


title: 293_pHelp_AAV_24hpi_rep_2

value: Mouse anti-Rep monoclonal (6 ug)


title: PDL1.HI3

description: Human CD4 Cells

value: peripheral blood derived CD4 cells


title: AND_42 [nasal]

description:
SYM042
Study subject 42 belonging to the AND group.

tag: gender

value: Female

value: Nasal biopsy


title: Ki67_aid_HCT116_Repliseq_late_r2

description:
Repli-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control; target: late.
Repliseq_6

value: control


title: Ctrl_604 [nasal]

description:
SAK604
Study subject 604 belonging to the Ctrl group.

tag: subject


title: APD_75 [nasal]

description:
SYM075
Study subject 75 belonging to the APD group.

tag: age


title: Ki67_aid_HCT116_Repliseq_late_r1

description:
Repli-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control; target: late.
Repliseq_2


title: PDL1.LO3

description: Human CD4 Cells

value: anti-CD3, anti-CD28, PDL1


title: IEI_4 [nasal]

description:
SYM004
Study subject 4 belonging to the IEI group.

value: IEI


title: Ki67_aid_HCT116_IAA_Repliseq_late_r1

description:
Repli-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA; target: late.
Repliseq_4


title: 293_pHelp_AAV_24hpi_rep_1

value: Kidney

value: Epithelial


title: PDL1.LO2

description: Human CD4 Cells


title: Sample 33_COVID-9

first: Shuibing

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description:
For viral genome
processed data file: raw_counts.covid.txt

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
For sample 1-6 and 28-33, Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b. Raw read counts were quantified using HTSeq-count v0.11.2.
For sample 7-27, the raw reads were aligned to human genome (GRCh38) using HISAT2 (version=2.1.0). The raw counts were extracted from bam files by featureCounts function (from package subread version=1.6.4).
Genome_build: GRCh38
Supplementary_files_format_and_content: plain txt file storing read counts per gene per sample

source_name: FFPE tissues

growth_protocol: Midbrain dopaminergic neuron differentiation were performed using H9 hESCs, which include Nurr1: GFP hESC.  hESCs were grown on VTN-N (Thermo Fisher Scientific)-coated 6-well plates in E8-essential medium. Cells were maintained at 37℃, 5% CO2. hESCs were differentiated with an optimized protocol from a previously reported study

extract_protocol:
Total RNA samples were prepared from cells and using TRIzol according to the manufacturer’s instructions.
RNAseq libraries of polyadenylated RNA were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions and sequenced on an Illumina NextSeq 500 platform.

treatment_protocol: For drug treatment, DA neurons were infected with SARS-CoV-2 at six hours post-treatment.

value: human ventral midbrain tissue

tag: viral infected

value: COVID19 patient

value: no


title: ESC-CTCF-rep2

description: CUT&TAG

data_processing:
CTCF CUT&TAG data analysis. Raw reads were trimmed using TrimGalore (version 0.4.4) with default parameters and aligned to the mouse genome (mm9) using bowtie2 (version 2.3.4.1) with parameters “--local --very-sensitive -I 10”. Unmapped reads and PCR duplicates were removed. Peaks were called using MACS2 (version 2.1.1.20160309) with parameters “-q 0.05 --nomodel --nolambda --extsize 120 -B --SPMR -g mm”.
mm9
bigWig

extract_protocol: CTCF ChIP-seq libraries were prepared using CUT&Tag developed by Kaya-Okur et al., Nat Protoc 2020 (PMID: 32913232).

treatment_protocol: mESCs containing a stably integrated transgene (MERVL::tdTomato) were cultured on 0.1% gelatin in DMEM containing 15% FBS, leukemia inhibiting factor (LIF), penicillin/streptomycin, L-glutamine, β-mercaptoethanol, and non-essential amino acids. After digestion with 0.05% trypsin, ESCs (non-2CLCs) and 2CLCs were sorted using the fluorescent reporters. The cells were then lysed for CUT&TAG.

value: 129/Ola, XY

value: CTCF


title: U2OS_AAV_24hpi_gh2ax_2

tag: disease

value: Osteosarcoma

value: Bone

tag: cell type

value: Millipore #05-636 (5 ug)


title: APD_73 [nasal]

description:
SYM073
Study subject 73 belonging to the APD group.

value: adult-onset asthma


title: U2OS_AAV_24hpi_gh2ax_1

tag: chip antibody


title: 293_AAV_24hpi_rep_2

value: Mouse anti-Rep monoclonal (6 ug)


title: CTCF-AID-2d-ESC-RNA-seq-rep2


title: Ki67_aid_HCT116_IAA_Repliseq_early_r1

description:
Repli-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control_IAA; target: early.
Repliseq_3

extract_protocol:
1. pA-DamID: 1 million permeabilized cells were processed with pA-DamID (van Schaik, 2020) with a primary antibody and for a Dam control condition, to specifically deposit m6A marks at chromatin nearby the primary antibody. Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit; 2. RNA-seq: RNA was isolated using the Qiagen RNeasy column purification kit; 3. Repli-Seq: cells were harvested as for pA-DamID and immediately fixed in ice-cold ethanol.
1. pA-DamID: the full protocol is described in Leemans, 2019, except that the DpnII digestion is omitted. 500 ng of genomic DNA was digested at m6A-methylated GATC sequences with DpnI and ligated to adapters. DNA fragments were amplified and further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 10-12 PCR cycles with illumina index adapters; 2: RNA-seq: sequencing libraries were prepared using the Illumina TruSeq polyA stranded RNA kit; 3: replicated DNA was enriched for with a BrdU IP, before libraries were prepared as described in Marchal, 2018.

value: Colorectal carcinoma cells

value: Repli-seq

tag: genetic modification

value: OsTir1; Ki67-miniAID-mClover

value: early


title: U2OS_AAV_36hpi_rep_2


title: U2OS_AAV_24hpi_input


title: AAD_12 [nasal]

description:
SYM012
Study subject 12 belonging to the AAD group.

value: Female

value: Nasal biopsy


title: IEI_2 [nasal]

description:
SYM002
Study subject 2 belonging to the IEI group.

value: IEI


title: IEI_8 [nasal]

description:
SYM008
Study subject 8 belonging to the IEI group.


title: Sample 30_COVID-5

value: human ventral midbrain tissue


title: APD_72 [nasal]

description:
SYM072
Study subject 72 belonging to the APD group.


title: 2CLC-CTCF-rep2

description: CUT&TAG


title: CTCF-AID-2d-ESC-RNA-seq-rep1


title: IEI_47 [nasal]

description:
SYM047
Study subject 47 belonging to the IEI group.


title: Pear1-/- Bleomycin, rep3

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing:
Quality checl of raw reads by FastQC
fragments per kilobase of exon per million mapped fragments
variance stabilizing transformation (VST) from the fitted dispersion-mean relation
eBayes moderated t-test
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: raw reads counts and normalized gene expression values in .txt format

source_name: Pear1-/- Bleomycin

extract_protocol:
Sorting out CD140a+ cells from mouse lung by flow cytometery
Cells were harvested and washed by PBS, following RNA extraction by TRIzol (Invitrogen) according to the manufactory's instructions.
SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc.) was used for generating high-quality, full-length cDNA from low amount of RNA.Then library was constructed using TruePrep TM DNA Library Prep Kit V2 for Illumina (Vazyme TD502).

tag: Sex

value: Male

value: Lung

value: Cd140a+ Lung mesenchymal cells

tag: genotype

value: Bleomycin


title: Pear1-/- Bleomycin, rep2

tag: treatment


title: 293_AAV_24hpi_rep_1

value: Kidney

value: Epithelial


title: 2CLC-CTCF-rep1

description: CUT&TAG

value: 129/Ola, XY

tag: transgene

value: CTCF


title: U2OS_AAV_36hpi_gh2ax_1

value: Osteosarcoma

value: Bone

value: Millipore #05-636 (5 ug)


title: ESC-CTCF-rep1

description: CUT&TAG


title: Wild-type Bleomycin, rep3

source_name: Wild-type Bleomycin

value: wild-type


title: APD_59 [nasal]

description:
SYM059
Study subject 59 belonging to the APD group.

value: adult-onset asthma


title: APD_36 [nasal]

description:
SYM036
Study subject 36 belonging to the APD group.

value: Female


title: Ki67_aid_HCT116_Repliseq_early_r1

description:
Repli-seq on HCT116 (ATCC CCL-247) cells (OsTir1; Ki67-miniAID-mClover); experiment: Ki67_aid; condition: control; target: early.
Repliseq_1

value: Colorectal carcinoma cells

tag: library type

value: Repli-seq

value: OsTir1; Ki67-miniAID-mClover

tag: experiment

tag: condition

value: control

value: early


title: U2OS_24hpd_input

tag: tissue


title: Ctrl_618 [nasal]

description:
SAK618
Study subject 618 belonging to the Ctrl group.

tag: diagnosis

value: healthy

value: Nasal biopsy


title: Sample 32_COVID-8

value: human ventral midbrain tissue

value: COVID19 patient

value: no


title: U2OS_AAV_36hpi_gh2ax_2

value: Epithelial


title: U2OS_24hpd_hu_gh2ax_2

value: Osteosarcoma


title: Sample 29_COVID-4


title: AAD_43 [nasal]

description:
SYM043
Study subject 43 belonging to the AAD group.

tag: gender


title: Pear1-/- Bleomycin, rep1

value: Male

value: Lung

value: Cd140a+ Lung mesenchymal cells

value: Bleomycin


title: Ctrl_602 [nasal]

description:
SAK602
Study subject 602 belonging to the Ctrl group.

value: Female

tag: subject


title: Sample 31_COVID-6


title: U2OS_AAV_36hpi_rep_1

value: Bone

value: Mouse anti-Rep monoclonal (6 ug)


title: U2OS_AAV_24hpi_rep_1


title: Sample 28_COVID-1


title: U2OS_AAV_24hpi_rep_2


title: Wild-type Bleomycin, rep1

value: wild-type


title: AND_64 [nasal]

description:
SYM064
Study subject 64 belonging to the AND group.

value: adult-onset asthma

tag: age


title: Sample 22_COVID#6

description:
For human genome
processed data file: raw_counts.patient_neuron.txt

tag: viral infected


title: Sample 23_COVID#8


title: Sample 27_non-COVID2

value: non-COVID19 patient


title: U2OS_24hpd_hu_gh2ax_1

tag: disease

value: Millipore #05-636 (5 ug)


title: Sample 26_non-COVID1

tag: cell type


title: Wild-type Vehicle, rep2

source_name: Wild-type Vehicle

value: Vehicle


title: Ctrl_631 [nasal]

description:
SAK631
Study subject 631 belonging to the Ctrl group.

value: healthy

value: Nasal biopsy


title: Wild-type Vehicle, rep1


title: AAD_76 [nasal]

description:
SYM076
Study subject 76 belonging to the AAD group.


title: Ctrl_627 [nasal]

description:
SAK627
Study subject 627 belonging to the Ctrl group.


title: AND_67 [nasal]

description:
SYM067
Study subject 67 belonging to the AND group.


title: Sample 25_non-COVID3

value: human ventral midbrain tissue

value: no


title: Pear1-/- Vehicle, rep3

source_name: Pear1-/- Vehicle


title: U2OS_24hpd_hu_rep_2

value: Osteosarcoma

value: Epithelial

tag: chip antibody


title: Ptri_SS_10G

first: Liudmila

last: Mikheeva

address: Wivenhoe Park

institute: University of Essex

data_processing:
Trimmed reads were aligned to Phaeodactylum tricornutum CCAP 1055/1 genome (GCF_000150955.2) using TopHat v2.1.2 with Bowtie2 v2.3.4.1. We used Picard tools (http://broadinstitute.github.io/picard/) to deduplicate reads and HTseq to count reads with parameters stranded=yes and type=exon.
Genome_build: Phaeodactylum tricornutum CCAP 1055/1
Supplementary_files_format_and_content: raw counts text files

organism: Phaeodactylum tricornutum

source_name: cell suspension

growth_protocol: Phaedactylum tricornutum was grown in K medium (Keller et al., 1987) with the addition of silicic acid (1.06 10-4 M) using an artificial seawater base and maintained under continuous illumination of 325±25 µmol photons m2 s-1.

extract_protocol:
Tri-Reagent as per manufacturers instructions including a DNAse treatment step
Preparation of dual-indexed, strand-specific RNASeq library from total RNA, using RiboZero rRNA depletion and the NEBNext Ultra Directional RNA library preparation kits according to manufacturet's instructions. Carried out by the centre for genomic research at the University of Liverpool.

treatment_protocol: Phaedactylum tricornutum was maintained in semi-continuous growth for more than 10 generations at three temperatures (10, 20 and 26.5 °C).

tag: temperature treatment (degree c)

tag: biological replicate

value: G

tag: strain

value: CCMP 2561


title: Sample 18_dopamine-Metformin3

description: processed data file: raw_counts.dopamine.txt

source_name: Neural cells

value: Dopaminergic Neuron

value: SARS-Cov-2 infected 48 hours

tag: treatment

value: Metformin


title: U2OS_24hpd_hu_rep_1

source_name: Epithelial

value: Bone

value: Mouse anti-Rep monoclonal (6 ug)


title: 293_24hpd_input

value: Kidney


title: APD_26 [nasal]

description:
SYM026
Study subject 26 belonging to the APD group.

source_name: Nasal biopsy

value: adult-onset asthma

value: Female


title: Ptri_SS_10C

value: C


title: 293_24hpd_gh2ax_2

value: Millipore #05-636 (5 ug)


title: 293_24hpd_gh2ax_1


title: Wild-type Bleomycin, rep2

tag: Sex

value: Male

value: Lung

value: Cd140a+ Lung mesenchymal cells

tag: genotype

value: wild-type

value: Bleomycin


title: APD_71 [nasal]

description:
SYM071
Study subject 71 belonging to the APD group.

value: Nasal biopsy


title: U2OS_24hpd_gh2ax_2

value: Osteosarcoma

value: Epithelial


title: Sample 15_dopamine-imatinib3

value: Dopaminergic Neuron

value: SARS-Cov-2 infected 48 hours

value: imatinib


title: 293_24hpd_rep_2

value: Mouse anti-Rep monoclonal (6 ug)


title: Wild-type Vehicle, rep3

value: Vehicle


title: Ctrl_615 [nasal]

description:
SAK615
Study subject 615 belonging to the Ctrl group.

value: healthy


title: Ptri_SS_10F

value: F

value: CCMP 2561


title: U2OS_24hpd_gh2ax_1

value: Bone

value: Millipore #05-636 (5 ug)


title: Sample 21_COVID#5

value: human ventral midbrain tissue

value: COVID19 patient

value: no


title: U2OS_24hpd_rep_1


title: IEI_14 [nasal]

description:
SYM014
Study subject 14 belonging to the IEI group.

value: IEI

value: Female


title: AAD_16 [nasal]

description:
SYM016
Study subject 16 belonging to the AAD group.

value: adult-onset asthma

value: Nasal biopsy


title: Pear1-/- Vehicle, rep2

value: Male

value: Lung

value: Cd140a+ Lung mesenchymal cells


title: IEI_5 [nasal]

description:
SYM005
Study subject 5 belonging to the IEI group.


title: Ptri_SS_26D

value: D


title: Sample 24_COVID#9


title: Pear1-/- Vehicle, rep1

value: Vehicle


title: Sample 13_dopamine-imatinib1

value: Dopaminergic Neuron

value: SARS-Cov-2 infected 48 hours

value: imatinib


title: Ptri_SS_26E

value: E

value: CCMP 2561


title: AND_56 [nasal]

description:
SYM056
Study subject 56 belonging to the AND group.


title: Sample 12_dopamine-Riluzole3

value: Riluzole


title: U2OS_24hpd_rep_2

value: Osteosarcoma

value: Bone

value: Epithelial

value: Mouse anti-Rep monoclonal (6 ug)


title: Sample 11_dopamine-Riluzole2


title: Ptri_SS_26A

value: A


title: Ptri_SS_20F

value: F


title: Sample 16_dopamine-Metformin1

value: Metformin


title: Sample 20_COVID#4

value: human ventral midbrain tissue

value: COVID19 patient

value: no


title: Ptri_SS_10B

value: B


title: Sample 17_dopamine-Metformin2

value: Dopaminergic Neuron


title: Ptri_SS_20E


title: Ctrl_638 [nasal]

description:
SAK638
Study subject 638 belonging to the Ctrl group.

value: healthy

value: Female

value: Nasal biopsy


title: Sample 19_COVID#1


title: AAD_65 [nasal]

description:
SYM065
Study subject 65 belonging to the AAD group.

value: adult-onset asthma


title: AND_45 [nasal]

description:
SYM045
Study subject 45 belonging to the AND group.


title: Ptri_SS_20B

value: CCMP 2561


title: Early_OA_painful

city: Bath

first: Amel

last: Badoume

address: Claverton Down

department: Pharmacy and Pharamcology

institute: University of Bath

description: 3' cDNA

data_processing:
Basecalls performed using cellranger mkfastq (cellranger version 3.0.1)- based on Illumina's bcl2fastq (v2.20)
cellranger count used to perform alignment and barcode and UMI counting. Indexed BAM file outputted with position-sorted reads aligned to the genome.
Genome_build: hg38
Supplementary_files_format_and_content: bam files- containing reads aligned to the genome and transcriptome annotated with barcoded information

source_name: Fibroblasts

growth_protocol: Synovial fibroblasts were cultured from diced synovial tissue in RMPI 1640 supplemented with 10% FSC, 5% non-essential amino acids, 5% L-glutamine, 5% sodium pyruvate and 1% penicillin/ streptomycin.

extract_protocol:
Passaged fibroblasts were harvested for single-cell RNA sequencing at 70-80% confluence.
3' cDNA libraries were prepared as per 10X Chromium Single Cell 3' Library Kit v2. Cells were pooled from each condition  (n=4), isolalated from a total of 4247 cells (roughly 353 cells/patient). Libraries were pooled and sequenced across 4 lanes.
Single-cell RNA sequencing- 10X Genomics

value: Synovial tissue

value: Synovial fibroblasts

tag: disease state

value: Knee osteoarthritis


title: Ptri_SS_20A

city: Colchester


title: Ptri_SS_26C

value: C


title: Sample 7_dopamine-DMSO1

value: SARS-Cov-2 infected 48 hours

value: DMSO


title: Sample 14_dopamine-imatinib2

value: imatinib


title: 293_24hpd_rep_1

description: The mouse anti-Rep monoclonal antibody has been generated and validated by the Pintel lab using western blots and immunofluorescence.

value: Kidney

value: Epithelial

value: Mouse anti-Rep monoclonal (6 ug)


title: T3_10

tag: control (c) or treatment (t)

value: T

tag: time point


title: T2_08


title: AAD_31 [nasal]

description:
SYM031
Study subject 31 belonging to the AAD group.

tag: diagnosis

tag: tissue


title: Sample 10_dopamine-Riluzole1

value: Dopaminergic Neuron

value: Riluzole


title: EndStage_OA_painful

description: 3' cDNA


title: JP21-MI

city: Birmingham

first: Susanne

middle: N

last: Wijesinghe

address: Mindelsohn Way

department: Institute of Inflammation and Ageing

institute: University of Birmingham

data_processing:
Illumina NextSeq 500 used for basecalling.
RNA-sequencing data was imported to the Galaxy web platform, usegalaxy.org, where sequences were mapped to GRCh38.p13 with HISAT2.
Raw count matrix generated using htseq-count on Galaxy web platform.
Trimmed Mean of M values (TMM) and TMM normalisation was performed using Qlucore Omics Explorer v3.6 (Qlucore AB, Lund, Sweden) where differential gene expression and pathway analysis were performed following TMM normalisation.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: TMM_normalised_counts.txt: Tab-delimited text file includes TMM values for each Sample.
Supplementary_files_format_and_content: Raw_gene_count_matix.txt: Matrix table with raw counts for every gene and every sample.

source_name: Osteoarthritic Knee Synovium

extract_protocol:
Synovium tissue was removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Lexogen’s QuantSeq 3’ kit was used for the construction of sequencing libraries.

value: Osteoarthritic Knee Synovium

value: Early OA

tag: pain level

value: Pain


title: JP26-LI


title: Sample 5_dpamine neuron-48h-H-2

last: Chen

description: processed data file: raw_counts.dpamine_neuron-48h.txt

value: no


title: Sample 9_dopamine-DMSO3


title: Ctrl_624 [nasal]

description:
SAK624
Study subject 624 belonging to the Ctrl group.

value: healthy

tag: gender

value: Female

tag: age

value: Nasal biopsy

tag: subject


title: Ctrl_622 [nasal]

description:
SAK622
Study subject 622 belonging to the Ctrl group.


title: Sample 4_dpamine neuron-48h-H-1

tag: cell type

tag: viral infected


title: Sample 6_dpamine neuron-48h-H-3


title: AND_81 [nasal]

description:
SYM081
Study subject 81 belonging to the AND group.

value: adult-onset asthma


title: APD_82 [nasal]

description:
SYM082
Study subject 82 belonging to the APD group.


title: Early_OA_non-painful

description: 3' cDNA

value: Synovial tissue

value: Synovial fibroblasts

value: Knee osteoarthritis


title: JP23-LS

value: End-stage OA

value: No-Pain


title: JP22-LS


title: JP23-MI


title: IEI_25 [nasal]

description:
SYM025
Study subject 25 belonging to the IEI group.

value: IEI


title: JP22-MS


title: C3_09

value: C

value: CCMP 2561


title: Ctrl_617 [nasal]

description:
SAK617
Study subject 617 belonging to the Ctrl group.


title: Sample 8_dopamine-DMSO2

description: processed data file: raw_counts.dopamine.txt

value: Dopaminergic Neuron

value: SARS-Cov-2 infected 48 hours

value: DMSO


title: AND_61 [nasal]

description:
SYM061
Study subject 61 belonging to the AND group.


title: Sample 2_dpamine neuron-48h-mock-2


title: Sample 3_dpamine neuron-48h-mock-3


title: JP18-MS

value: Osteoarthritic Knee Synovium

value: Early OA

value: Pain


title: T4_12

value: T


title: JP20-MS


title: C1_08


title: T4_11


title: HCT116_NC3

city: shijiazhuang

first: liang

middle: hui

last: zhi

state: hebei

address: zhongshanxilu

institute: Bethune International Peace Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；mRNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 3.4.3
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

growth_protocol: Cells were cultured with DMEM supplemented with 10% fetal bovine serum and penicillin-streptomycin at 37℃ in 5% CO2 and 95% air

extract_protocol:
Total RNA was extracted from HCT116 cells using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell s were transfected with the short interfering RNA (siRNA) specific for SLCO1B3 or negative control according to the manufacturer's instructions.

tag: cell line

value: Colorectal cancer cell

tag: target sequences

tag: group

value: control


title: JP20-LS


title: T4_03

tag: biological replicate

tag: strain


title: T1_12


title: T4_10


title: Sample 1_dpamine neuron-48h-mock-1

value: no

tag: treatment


title: HCT116_NC5


title: JP21-LI


title: APD_41 [nasal]

description:
SYM041
Study subject 41 belonging to the APD group.

value: adult-onset asthma

value: Female

value: Nasal biopsy


title: AAD_58 [nasal]

description:
SYM058
Study subject 58 belonging to the AAD group.


title: JP18-LS

value: No-Pain


title: JP16-LS


title: T4_09


title: JP16-MS


title: IEI_37_A [nasal]

description:
SYM037_A
Study subject 37_A belonging to the IEI group.

value: IEI


title: HCT116_NC1


title: AAD_13 [nasal]

description:
SYM013
Study subject 13 belonging to the AAD group.


title: HCT116_si5


title: AND_79 [nasal]

description:
SYM079
Study subject 79 belonging to the AND group.


title: IEI_3 [nasal]

description:
SYM003
Study subject 3 belonging to the IEI group.


title: AAD_77 [nasal]

description:
SYM077
Study subject 77 belonging to the AAD group.


title: JP12-MI

value: End-stage OA


title: HCT116_si3


title: T4_07

value: CCMP 2561


title: AND_39 [nasal]

description:
SYM039
Study subject 39 belonging to the AND group.


title: JP12-LI


title: HCT116_si1


title: Ctrl_619 [nasal]

description:
SAK619
Study subject 619 belonging to the Ctrl group.

value: healthy


title: T4_06


title: JP07-MS


title: Ventral Fusion Region Day 90

city: Vienna

first: Sunanjay

last: Bajaj

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Institute for Molecular Biotechnology of the Austrian Academy of Sciences

data_processing:
Reads aigned to GRCh38 human reference genome with Cell Ranger 3.1
UMI counts were then analyzed using the Seurat R package v.3.
As described previously (Kanton et al., 2019), we excluded clusters with ‘glycolysis’ identity based on GO-enrichment of cluster specific marker genes.
Variable genes were identified by Seurat's FindVariableFeatures implementation (“FastLogVMR”)
Next, principal components were calculated on the variable genes, and the first 50 components were then used to calculate UMAP coordinates.
Genome_build: GRCh38

source_name: Cerebral Organoid Fusion

growth_protocol: Cerebral organoid fusions (Fusions) were generated with a modified protocol, expanding upon previous organoid generation protocols from our lab (Lancaster et al., 2013, 2017). Please see methods of manuscript for details.

extract_protocol:
Organoid Fusions were first manually dissected. Tissue was then dissociated by a 30min incubation at 37 oC  at 800rpm shaking speed on a ThermoMixer® . GFP+ cells were then obatiend via FACS.
Libraries were generated with the 10x Chromium Single cell 3’ GEM, Library & gel Bead Kit v3 (10x Genomics, cat. #PN-1000075). Libraries were pooled and sequenced on a NovaSeq S1 flow cell (Illumina) with 2.6-3.2 billion paired-end reads.

tag: stem cell type

value: H9 Feeder Free Human ESCs

tag: sample type

value: ventral


title: Ventral Fusion Region Day 70


title: T4_04

tag: control (c) or treatment (t)

tag: time point


title: T4_08


title: T4_05


title: Dorsal Fusion Region Day 90

value: dorsal


title: JP05-LS

tag: tissue

value: Osteoarthritic Knee Synovium

tag: diagnosis


title: JP05-LI

tag: pain level


title: APD_63 [nasal]

description:
SYM063
Study subject 63 belonging to the APD group.

tag: gender

tag: age


title: Ctrl_603_A [nasal]

description:
SAK603_A
Study subject 603_A belonging to the Ctrl group.

tag: subject


title: T4_01


title: T4_02


title: sg2_input

first: Jinyang

last: Li

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
alignment using Bowtie2 to generate sam files
sam and bam files were processed with SAMtools
eak calling using MACS2
peaks were merged with BEDTools
read counts were calculated and normalized in the merged peaks for every sample
Genome_build: hg38
Supplementary_files_format_and_content: normalized count for each peaks across samples

growth_protocol: MOLM-13 cell line was cultured in RPMI (Corning, 10-041-CV) with 10% FBS (Life Technologies, 16000044) and 1% Penicillin Streptomycin (Gibco, 15-140-122).

extract_protocol:
ChIP-seq samples were prepared following standard protocol in this manuscript.
ChIP-seq libraries were prepared following the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) protocol, using NEBNext Multiplex Oligos Index Primers Sets

treatment_protocol: MOLM-13 cells were transduced with lentivirus containing CRISPR-Cas9 EV or sgKAT6A for 4 days.

tag: transduced

tag: antibody


title: T4_00


title: JP02-MS

value: Early OA

value: Pain


title: Dorsal Fusion Region Day 70


title: JP07-LS

value: Low pain


title: sg2_K9ac.no2


title: IEI_55 [nasal]

description:
SYM055
Study subject 55 belonging to the IEI group.


title: JP02-LS


title: APD_44 [nasal]

description:
SYM044
Study subject 44 belonging to the APD group.


title: C4_12

value: C


title: C4_11


title: sg2_K23ac.no2


title: Ctrl_601 [nasal]

description:
SAK601
Study subject 601 belonging to the Ctrl group.


title: AAD_68_A [nasal]

description:
SYM068_A
Study subject 68_A belonging to the AAD group.


title: AND_54 [nasal]

description:
SYM054
Study subject 54 belonging to the AND group.


title: JP01-MI


title: Basal-like triple-negative breast cancer cell line, SUM149

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

address: 203 E Cary St

institute: Virginia Commonwealth University

description:
Sample 8
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Merged_PDX_TNBC_XPO1subset_DeadFilt_GRCh38.cloupe

data_processing:
Basecalling: BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14)
QC: Fastq files containing the read were analyzed with FastQC v.0.11.8 to identify any quality concerns with the raw data.
Alignment (PDX): Fastq files from PDX samples (HCI1, UCD52, WHIM2, WHIM30) were aligned independently to the merged human/mouse hg19mm10 genome provided by 10X using CellRanger v3.1 "count" algorithm with the expected number of cells set to 5000.
Alignment (TNBC): Fastq files from TNBC samples (HCC1143, HCC1187, MDA468, SUM149) were aligned independently to the GRCh38 human genome provided by 10X using CellRanger v3.1 "count" algorithm with the expected number of cells set to 5000.
Mouse Cell Removal (PDX): An in-house R script and the 10X-generated GEM file were used to identify and remove all mouse and multiplet cell barcodes from each PDX sample by using the CellRanger script "subset_bam".  The remaining reads were converted back to fastq files using the CellRanger script "bamtofastq".  These new filtered fastq files were then re-aligned independently to the GRCh38 human genome using the CellRanger "count" algorithm, however, this time the Force Cells option was set to the exact number of remaining human cells for each sample.
Dead Cell Removal (PDX and TNBC): An in-house R script using the Seurat v4 R package was used to identify and remove barcodes associated with dead or poor quality cells.  The 10X "subset_bam" and "bamtofastq" scripte were once again used to filter the bam files for each sample to generate fastq files containing only the reads from good quality human cells.
Alignment (PDX and TNBC): Each sample was re-aligned to the human GRCh38 genome provided by 10X using the CellRanger "count" algorithm with the Force Cells option set to the exact number of good quality cells identified in the previous step.
Merging (PDX and TNBC): All samples were then merged into one file using the CellRanger "aggr" algorithm and default settings. Output includes the features, barcodes, and matrix files provided with this submission, along with a Loupe CellBrowser file.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data files are the merged data from all samples, and include the 10X formatted features.tsv.gz, barcodes.tsv.gz (barcode-#, where # refers to Sample #1-8), and matrix.mtx.gz files that can be imported directly into R using the Seurat package. Also a .cloupe file that can be viewed in the Loupe Cell Browser v4 and above.

growth_protocol: Cell lines were grown in Glutamax +10%FBS. PDXs were grown in NSG mice mammary glands and harvested when ~8mm in the largest dimension

extract_protocol:
10X Genomics 3' library kit v3.0
scRNA-Seq

treatment_protocol: Untreated

tag: cell type

value: Primary Patient Tumor (TNBC)


title: C4_10


title: AAD_11 [nasal]

description:
SYM011
Study subject 11 belonging to the AAD group.

value: adult-onset asthma


title: sg2_K14ac.no2

city: New York


title: C4_08


title: C4_09


title: sg2_K23ac.no1


title: sg2_K9ac.no1


title: Basal-like triple-negative breast cancer cell line, HCC1187

description:
Sample 6
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Merged_PDX_TNBC_XPO1subset_DeadFilt_GRCh38.cloupe


title: Basal-like triple-negative breast cancer cell line, HCC1143

description:
Sample 5
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Merged_PDX_TNBC_XPO1subset_DeadFilt_GRCh38.cloupe


title: JP01-MS


title: sg2_K14ac.no1


title: Basal-like triple-negative breast cancer patient-derived xenograft, WHIM30

description:
Sample 3
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Merged_PDX_TNBC_XPO1subset_DeadFilt_GRCh38.cloupe

value: Primary Tumor from Patient Derived Xenograft (PDX)


title: C4_07


title: C4_06


title: ev_K9ac.no2

value: CRISPR-Cas9 EV


title: APD_35 [nasal]

description:
SYM035
Study subject 35 belonging to the APD group.

value: Female

value: Nasal biopsy


title: Ctrl_621 [nasal]

description:
SAK621
Study subject 621 belonging to the Ctrl group.


title: ev_K9ac.no1


title: Basal-like triple-negative breast cancer cell line, MDA468

description:
Sample 7
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Merged_PDX_TNBC_XPO1subset_DeadFilt_GRCh38.cloupe


title: IEI_1 [nasal]

description:
SYM001
Study subject 1 belonging to the IEI group.

value: IEI


title: C4_05

value: CCMP 2561


title: Basal-like triple-negative breast cancer patient-derived xenograft, UCD52

description:
Sample 2
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Merged_PDX_TNBC_XPO1subset_DeadFilt_GRCh38.cloupe


title: C4_04


title: Basal-like triple-negative breast cancer patient-derived xenograft, WHIM2

description:
Sample 4
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Merged_PDX_TNBC_XPO1subset_DeadFilt_GRCh38.cloupe


title: ev_K23ac.no2


title: Ctrl_605 [nasal]

description:
SAK605
Study subject 605 belonging to the Ctrl group.

value: healthy


title: APD_63 [blood]

description:
SYM063
Study subject 63, cell sample.

source_name: PBMC

extract_protocol: Total RNA was isolated from 2x10^6 PBMCs by AllPrep Plus (Qiagen). Quantity and quality of the samples were determined by NanoDrop spectrophotometer and Agilent Bioanalyzer 2100, respectively. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.

treatment_protocol: PBMCs were extracted from the blood by CPT tubes. Several control individuals underwent 2 different treatments, one set used inhaled corticosteroids (SAKII, N = 15) and the others did not (SAK, N = 21).

value: PBMC


title: Basal-like triple-negative breast cancer patient-derived xenograft, HCI-001

description:
Sample 1
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
Merged_PDX_TNBC_XPO1subset_DeadFilt_GRCh38.cloupe

value: PDX


title: C4_03

treatment_protocol: See "overall design"


title: ev_K23ac.no1


title: ev_K14ac.no2


title: Ctrl_624 [blood]

description:
SAK624
Study subject 624, cell sample.


title: ev_input


title: C4_02


title: AND_67 [blood]

description:
SYM067
Study subject 67, cell sample.


title: Ctrl_611 [nasal]

description:
SAK611
Study subject 611 belonging to the Ctrl group.


title: C4_01


title: ev_K14ac.no1


title: AIII-C

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

data_processing:
Base calling using Illumina CASAVA software
Filtering of ribosomal and mitochondrial sequences and 5’end trimming of 2 bases (bowtie in TopHat Alignment  v1.0.1)
Assignment to genomic features (GenomicAlignment -R version 3.5.3)
Genome_build: Human GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text file with Ensembl ID and read counts for all the samples

source_name: Brain tumor

extract_protocol:
We deparaffined 3 slices of 10 µm-thickness from each FFPE-block according to the xylene protocol described in the RNeasy FFPE kit (Qiagen) handbook. Total RNA were obtained after purification and DNase digestion using the RNeasy FFPE kit (Qiagen) following manufacturer’s instructions.
The starting amount of total RNA was 100 ng following Illumina recommendations to prepare the sequencing library using the TruSeq RNA Exome library kit (Illumina).

treatment_protocol: No treatment

value: Astrocytoma grade III

value: Male


title: GB-A

value: Glioblastoma grade IV


title: MOLM-13.sgKAT6A.2

data_processing:
Alignment-independent quantification using Salmon
Genome_build: hg38
Supplementary_files_format_and_content: TPM as txt file

extract_protocol:
RNA was extracted using Qiagen RNeasy  Kit.
RNA-seq libraries were build by a commercial company, Novogene, following standard protocols.

treatment_protocol: Cells were transduced with lentivirus containing CRISPR-Cas9 EV or sgKAT6A.

tag: cell line


title: C4_00

tag: biological replicate


title: AIII-A


title: T3_12

value: T

tag: strain


title: GB-C


title: GS-C

value: Gliosarcoma of giant cells grade IV


title: MOLM-13.sgKAT6A.1

tag: treatment


title: MOLM-13.ev.2

value: ev


title: Ctrl_II631 [blood]

description:
SAKII631
Study subject II631, cell sample.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into eUtopia bioinformatics package and analyzed with BioConductor package Limma. Data was quantile normalized based on cutoff 0.75 and percentage of samples 75%. Replicate control probes were combined by their median values.


title: MOLM-13.ev.1


title: APD_33 [blood]

description:
SYM033
Study subject 33, cell sample.


title: APD_75 [blood]

description:
SYM075
Study subject 75, cell sample.