title: coro1a-DsRed cells,ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM), 30 hpf, smart-seq, rep1

description:
Library name: sample4
IK-myb-1
Wt-vs-DM.all.annot.txt

value: embryos coro1a-DsRed positive myeloid cells

value: myeloid cell

value: ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM)


title: K562_8332_single_0min_JH0021

status: Public on Sep 24 2025

type: SRA

city: Vienna

first: Jakob

last: Huemer

state: Vienna

address: Zimmermannpl. 10

country: Austria

institute: Children’s Cancer Research Institute

description:
1 K562 cells that did not interact
processed data file: Counts_PrimNK.csv

library_source: transcriptomic

data_processing:
Raw reads were trimmed using trimmomatic (version 0.32)
aligned to the mouse reference genome (mm10) using HISAT2 (version 2.1.0)
Uniquely mapped reads for each exon were counted using the function summarizeOverlaps from the Ge-nomicAlignments package (version 1.12.0) in R (version 3.4.0)
Gene and exon annotations were obtained from the Ensembl GENCODE Basic set (genome-build GRCh38)
Assembly: hg38
Supplementary files format and content: csv file of read counts

molecule: total RNA

organism: Homo sapiens

source_name: K562 cells

growth_protocol: Human primary NK cells (‘primary NK cells’) were isolated from buffe coat and enriched using RosetteSep Human NK Cell Enrichment Cocktail (Stemcell technologies) according to manufacturer’s instructions. Enriched NK cells were resuspended in PBS supplemented with 3% heat-inactivated fetal bovine serum and 10mM ultrapure EDTA, pH 8.0 (Invitrogen) and further purified with MagniSort Human NK cell Enrichment Kit (Invitrogen) according to manufacturer’s instructions. CD19-specific human CAR T cells (‘aCD19CAR cells’) were generated similarly as described before (Salzer et.al., 2020). Normal donor derived T cells were lentivirally transduced following 24 hours of stimulation with T Cell TransAct (Miltenyi Biotec) according to manufacturer’s protocol. Lentiviral supernatant was added at a final dilution of 1:4. Stimulation reagent was removed by centrifugation after 72 hours of activation. Transduced T cells were cultivated in AIM V medium (Thermo Scientific) with 2.5% 1M HEPES (Gibco), 2% heat-inactivated octaplas SD blood type AB (Vienna Red Cross), 1% L-Glutamine was supplemented with 10 ng/ml rh IL- 7 (Miltenyi Biotec) and 5 ng/ml rh IL-15 (Miltenyi Biotec) instead of 200 rh U/ml IL-2. CD19 specific CAR T cells were enriched for CD8+ population using MagniSort Human CD8 T cell Enrichment Kit (Invitrogen) according to manufacturer’s instructions. CAFs (‘CAF cells’) were isolated from a liver metastasis of an individual with colorectal cancer. The tumor metastasis was dissociated with 100 U/ml collagenase IV (Gibco) in DMEM supplemented with 10% fetal bovine serum for 1 hour at 37°C. Cells were strained through 0.45µm filter and grown for 2 hours in EGM-MV2 (PromoCell). Thereafter, cells were cultured in EGM-MV2 supplemented with 0.25 μg/ml amphotericin B (Gibco), 20 mg/ml gentamycin (Gibco), 100 U/ml penicillin/streptomycin (Sigma) with a daily 5 hours antibiotic free incubation period. From passage 2 onwards fibroblast were grown in EGM-MV2 without antibiotics. NK-92 cells (‘NK92 cells’) were cultured in alphaMEM (Sigma) supplemented with 12.5% heat-inactivated fetal bovine serum (Sigma), 12.5% heat-inactivated horse serum (Sigma), 0.2 mM myo-inositol, 0.02 mM folic acid, 10 mM HEPES (Gibco), 100 U/ml Penicillin-Streptomycin (Gibco), 2 mM L-glutamine (Sigma), and 20 U/ml rh IL-2 (Novartis). NK-92 cells were passaged every 2-3 days and given fresh medium 1 day before the experiments. K562 cells (‘K562 cells’) were grown in RPMI-1640 (Gibco) supplemented with 2 mM L-glutamine, 10 mM HEPES, 100 U/ml Penicillin-Streptomycin, and 10% heat-inactivated fetal bovine serum (further described as ‘full RPMI’). Jurkat cells (‘Jurkat cells’) were grown in full RPMI. CD19+ Jurkat cells were generated by CD19 mRNA electroporation similar to the previously described method (Zajc et. al., 2020).

extract_protocol:
RNA was isolated according to Smart-seq2 was performed as described previously (Picelli et.  al., 2014). In brief, cells were lysed in 0.2% Triton X-100 in the presence of RNase inhibitor 40 U/µl RNase inhibitor (Takara) and stored at -80°C until ready to proceed.
RNA was denatured, reverse transcribed and amplified for 22 cycles. After reverse transcription, 1 ng cDNA was tagmented, amplified and barcoded following the Illumina Nextera indexing strategy. Final libraries were pooled to 4 nM for sequencing on HiSeq3000/4000. cDNA and library quality was assessed using TapeStation 4150 instrument and D5000HS or D1000 screening tapes (Agilent), respectively. DNA concentration was determined using Qubit dsDNA HS kit and instrument (Invitrogen). cDNA and Illumina Nextera indexed samples were purified using Ampure XP beads (Beckman Coulter) at 1:1 ratio. Sequencing was performed by the Biomedical Sequencing Facility at CeMM at 50bp single-end configuration.

treatment_protocol: For CIPS application: Cells were brought to high viability and density by spinning at 100 rcf for 3 minutes and subsequent elution in full RPMI. 1 million cells were stained with Hoechst 3334 (Invitrogen) and to discriminate GFP-expressing K562 from NK-92 cells, NK-92 cells were in addition counterstained with CD56-PE (N901, Beckman Coulter) for 30 minutes in full RPMI. Cells were washed with PBS and brought to a density of 1000 cells per µl in full RPMI for loading on a DEPArray Cartridge V2 (Silicon Biosystems). Cells were scanned for brightfield, the corresponding fluorescent markers and Hoechst (DAPI) for doublet/multicell exclusion. For further use, cells were defined with the following parameters: (i) in ‘grid’ (one cell per DEP cage), (ii) Hoechst positive, and (iii) cell size. Cell fulfilling criteria (i) to (iii) were categorized as NK-92: smaller cells, GFP negative, PE positive or K562: bigger cells, GFP positive, PE negative. From this pool, approximately 50-60 cells each were moved the Cartridge ‘park area’, where cells were aligned, collided and separated by changing the electric potential of DEP cages. Cells were assigned and moved to RNase/DNase-free 0.2 ml PCR-tubes (Applied Biosystems). After total four hours of cell-cell interactions cells were washed by adding RNase-free PBS up to a total of 100 µl per sample. Cells were spun and the total volume was reduced to approximately 1 µl using the VRNxT/Silicon Biosystems (‘DEPArray OUT‘ program) according to the manufacturer’s instructions. Enriched primary human NK cells with K562 partner cell were stained and processed the same in the CIPS procedure as described above for NK-92 and K562 cells. Enriched CD8+ CD19 specific CAR T cells with Jurkat partner cell and CAFs processed with following adaptations. Enriched CD8+ CD19 specific CAR T were stained with Hoechst 3334, CD4-APC (clone RPA-T4, BD Biosciences), CD8-PE (clone SK1, BD Biosciences) and GFP-expressing Jurkat cells with Hoechst 3334. Cells were categorized as CD8+ T cells as: smaller cells, APC negative, PE positive or Jurkat: bigger cells, GFP positive, APC negative, PE negative. CAFs were stained with Hoechst 3334, CD90-APC (clone 5E10, Biolegend), FAP-AF488 (clone # 427819, R&D) and categorized as: bigger cells, APC positive, GFP dim. Cell manipulation, recovery was done as described before with longer routing times for primary human NK cells and CD8+ T cells. For FACS application: Enrichment of human primary NK cells, CD8+ CD19 specific CAR T cells and expression of CD19 on Jurkat cells was assessed using 100-200*10^3 cells and controls each. Cells were washed in 2% heat-inactivated fetal bovine serum in PBS after blocking for 10min, 4°C in 10% heat-inactivated fetal bovine serum in PBS. Cells were stained with the following antibodies at 4°C for 30min. Primary human NK cells: CD56-AF700 (clone B159, BD Biosciences) and CD3-FITC (clone SK7, BD Biosciences). CD19 specific CAR T cells: CD3-FITC (clone SK7, BD Biosciences), CD4-APC (clone RPA-T4, BD Biosciences), CD8-V450 (clone RPA-T8, BD Biosciences), and DYKDDDDK (Flag) Tag-PE (clone L5, Biolegend), the latter for CAR expression. CD19+ Jurkat cells: CD19-PECy7 (clone SJ25C1, BD Bioscience). Cells were washed and analyzed as well as  500 cell per well sorted for following populations. Primary NK cells: ‘CD56hi’, ‘CD56dim’; Jurkat cells: ‘Jurkat’, ‘CD19Jurkat’; CD19-specific human CAR T cells: ‘CD4pos’, ‘CD8pos’ using Aria Fusion. Following a degranulation assay NK-92 and K562 cells stained with stained with a CD56-AF700 and CD107a-PE antibody cells were washed, re-suspended, and filtered in 0.5% BSA in PBS. 500 cells of unresponsive NK-92 (CD56+, CD107a-), granule releasing NK-92 (CD56+, CD107a+) and K562 (GFP+) were sorted with Aria Fusion into a 96-well plate for follow-up Smart-seq2 processing. CD107a positivity was defined by NK-92 cells stimulated for two hours with 250 ng/ml Phorbol 12-myristate 13-acetate (PMA) and 1 µg/ml Ionomycin. NK-92 and K562 cells incubated alone were processed as negative controls. For both, CIPS and FACS application cells were further processed with the Smart-Seq2 protocol.

tag: cell type

value: K562 cells

tag: number of cells

tag: interaction duration

tag: experiment id

tag: genotype

value: WT

tag: phenotype

value: GFP

tag: treatment


title: HepG2-hCAR cells, DOX-2, 72 hours

city: Baltimore

first: Hongbing

last: Wang

state: Maryland

address: 20 Penn Street

country: USA

institute: University of Maryland, Baltimore

description:
Library name: DOX-2
column name in Expression_Gene_FPKM.txt: DOX-2

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software. The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown.
Assembly: GRCh37
Supplementary files format and content: text file includes FPKM values for each sample

source_name: HepG2-hCAR cells

growth_protocol: hCAR expression lentivirus plasmid was generated by cloning the full-length cDNA into the EcoRI site of a pCW57-GFP-2A-MCS lentiviral vector. For generation of Doxycycline (Dox-inducible CAR overexpression stable cell lines, HepG2 cells were infected with Dox-inducible CAR lentivirus for 72 h and then refed with fresh medium including the selection drug. Cells were refed every 2 days until uninfected control cells were completely killed, which took 4 to 5 days for puromycin (1 μg/ml). The positive infection cells were plated 1 cell/well in 96-well plate. The cells grown up from a single cell were selected, and Dox induction was tested again. The cell lines with the best Dox induction for overexpression of hCAR, named HepG2-hCAR, were selected for use in this study. HepG2-hCAR cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 μg/ml streptomycin in humidified incubator at 37 °C and 5% CO2.

extract_protocol:
RNA samples were isolated using the miRNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Total RNA was quantified using NanoDrop ND-1000 instrument.
About 1 to 2 μg of total RNA was used to prepare the sequencing library. In brief, total RNA is enriched by oligo (dT) magnetic beads (rRNA removed); RNA-Seq library was prepared by using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-Seq library strand specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification quantitative PCR method.

treatment_protocol: HepG2-hCAR cells were treated with vehicle control or Dox (1 μg/ml) for 72 h.

tag: cell line

value: HepG2-hCAR cells

value: human liver carcinoma cells

value: Doxycycline (1ug/ml)


title: C1498_45deg_5h_16

city: Kobe

first: Katsuyuki

last: Shiroguchi

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

description: Library name: Cell_ID_80

library_source: transcriptomic single cell

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Each library was sequenced twice, and the generated fastq files were merged for each library.
Reads were aligned to the mm10 genome assembly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Assembly: Mouse mm10
Supplementary files format and content: The calculated copy number of RNA moelcules per cell for each gene is listed.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
RNAs from cell lysate was directly used for library preparation.
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Microscopically observed headted cells were picked with ALPS.


title: HepG2-hCAR cells, DOX-3, 72 hours

description:
Library name: DOX-3
column name in Expression_Gene_FPKM.txt: DOX-3


title: C1498_45deg_5h_19

description: Library name: Cell_ID_83


title: C1498_45deg_5h_14

description: Library name: Cell_ID_78


title: Patient AC-001-029 CLL Progression PD-1-

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

description: Library name: AC-001-029_PD1lo

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed reads were aligned to the GRCh38 reference genome (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a
RseQC was used to assess strand specificity for all transcripts
HTSeq was used to estimate transcript abundance from unique mapped reads
Raw reads were normalized using DESeq2 v1.26.0
Assembly: GRCh38
Supplementary files format and content: Raw counts
Supplementary files format and content: normalized counts

source_name: Peripheral Blood

extract_protocol:
Previously frozen PBMC samples were thawed and stained with Live/Dead Fixable Near-IR Dead Cell Stain (Invitrogen) followed by antibodies directed against CD3, CD19, CD20, CD5, and PD-1. Cells were sorted into RLT buffer at the Emory University School of Medicine Flow Cytometry core using a BD FACSAria II. RNA isolation, library preparation, and sequencing were performed by the Emory University National Primate Center Nonhuman Primate Genomics Core at Emory University.
SMART-Seq v4 Ultra Low Input RNA Kit with Illumina's Nextera XT DNA Library preparation kit

treatment_protocol: Samples were obtained from patients who were 1) treatment naïve, 2) on BTK inhibitors, or 3) progressing from BTK inhibitors

tag: tissue

value: Peripheral Blood

tag: cell

value: CLL cell

value: Tumor cell

tag: condition

value: Progressor

tag: disease

value: Chronic Lymphocytic Leukemia

tag: FISH

value: del13q, del11q, Trisomy.12

tag: ighv

value: Unmutated

tag: patient id


title: Patient AC-002-047 CLL Progression PD-1-

description: Library name: AC-002-047_PD1lo

value: del11q, del17p


title: HepG2-hCAR cells, DOX-1, 72 hours

description:
Library name: DOX-1
column name in Expression_Gene_FPKM.txt: DOX-1


title: HepG2-hCAR cells, con-3, 72 hours

description:
Library name: con-3
column name in Expression_Gene_FPKM.txt: con-3

value: vehicle control


title: K562_816_p19_15min_JH00013_S65181

description:
1 K562 cells that interacted for 15min
processed data file: Counts_NK92.csv


title: K562_8086_t1_c1_5min_JH00014_S65130

description:
1 K562 cells that interacted for 5min
processed data file: Counts_NK92.csv


title: Patient AC-002-040 CLL Progression PD-1-

description: Library name: AC-002-040_PD1lo

value: Mutated


title: C1498_45deg_5h_12

description: Library name: Cell_ID_76


title: Patient AC-002-040 CLL Progression PD-1+

description: Library name: AC-002-040_PD1hi


title: Patient AC-002-047 CLL Progression PD-1+

description: Library name: AC-002-047_PD1hi

value: Normal


title: HepG2-hCAR cells, con-2, 72 hours

description:
Library name: con-2
column name in Expression_Gene_FPKM.txt: con-2


title: C1498_45deg_5h_15

description: Library name: Cell_ID_79


title: K562_771_p2_3min_JH00010_S65248

description:
1 K562 cells that interacted for 3min
processed data file: Counts_NK92.csv

value: K562 cells


title: C1498_45deg_5h_11

description: Library name: Cell_ID_75


title: K562_7500_p8_5min_JH0021

description:
1 K562 cells that interacted for 5min
processed data file: Counts_PrimNK.csv

value: WT


title: Patient AC-001-110 CLL Progression PD-1+

description: Library name: AC-001-110_PD1hi


title: Patient AC-001-038 CLL Progression PD-1+

description: Library name: AC-001-038_PD1hi


title: C1498_45deg_5h_10

description: Library name: Cell_ID_74


title: C1498_45deg_5h_9

description: Library name: Cell_ID_73


title: HepG2-hCAR cells, con-1, 72 hours

description:
Library name: con-1
column name in Expression_Gene_FPKM.txt: con-1


title: Brain, SSDS+shACOT12, ventral hippocampus, rep2

city: wuhan

first: yu

last: cao

address: Qiaokou District

country: China

institute: Huazhong University of Science and Technology

description:
Library name: Sample 11
Column name in raw_All_Samples.txt: TBG_shACOT12_2

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) accordingtothe manufacturer’s instructions. After cluster generation, the library preparations weresequenced on an Illumina Novaseq platform and 150 bp paired-end reads weregenerated
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data (clean reads) were obtained by removing readscontaining adapter, reads containing ploy-N and low quality reads fromrawdata. Atthe same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a databaseof splice junctions based on the gene model annotation file and thus a better mappingresult than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene. FPKM, expected number of Fragments PerKilobase of transcript sequence per Millions base pairs sequenced, considers theeffect of sequencing depth and gene length for the reads count at the same time, andiscurrently the most commonly used method for estimating gene expression levels
Differential expression analysis of twoconditions/groups (two biological replicates per condition) was performed usingtheDESeq2 R package (1.16.1). DESeq2 provide statistical routines for determiningdifferential expression in digital gene expression data using a model based onthenegative binomial distribution. The resulting P-values were adjusted using theBenjamini and Hochberg’s approach for controlling the false discovery rate . Geneswith an adjusted P-value <0.05 found by DESeq2 were assigned as differentiallyexpressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files includes FPKM values for each Sample

source_name: ventral hippocampus

extract_protocol:
Total RNA was obtained from the tissues using standard extraction methods and RNA integrity was assessed using the RNA Nano 6000 Assay Kit on the Agilent 2100 Bioanalyzer system.
A total amount of 1 µg RNA per sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations and index codes were added to attribute sequences to each sample.

value: ventral hippocampus


title: C1498_45deg_5h_8

description: Library name: Cell_ID_72


title: Brain, SSDS+shACOT12, ventral hippocampus, rep3

description:
Library name: Sample 12
Column name in raw_All_Samples.txt: TBG_shACOT12_3


title: K562_7_p3_11_5min_JH0020

description:
1 K562 cells that interacted for 11.5min
processed data file: Counts_PrimNK.csv

value: GFP


title: Brain, SSDS+shACOT12, ventral hippocampus, rep1

description:
Library name: Sample 10
Column name in raw_All_Samples.txt: TBG_shACOT12_1


title: K562_698_p3_4min_JH00010_S65249

description:
1 K562 cells that interacted for 4min
processed data file: Counts_NK92.csv


title: K562_669_p4_2min_JH00010_S65250

description:
1 K562 cells that interacted for 2min
processed data file: Counts_NK92.csv


title: C1498_45deg_5h_13

description: Library name: Cell_ID_77


title: Patient AC-001-105 CLL treatment-naïve PD-1-

description: Library name: 6_AC-001-105-PD-1neg_S24

value: treatment-naïve


title: C1498_45deg_5h_7

description: Library name: Cell_ID_71


title: Patient AC-001-051 CLL treatment-naïve PD-1-

description: Library name: 9_AC-001-051-PD-1neg_S27


title: Patient AC-001-029 CLL Progression PD-1+

description: Library name: AC-001-029_PD1hi


title: C1498_45deg_5h_6

description: Library name: Cell_ID_70


title: Patient AC-001-107 CLL treatment-naïve PD-1-

description: Library name: 30_AC-001-107_PD-1neg_S48

value: Trisomy 12


title: K562_6317_p5_10min_MF224

description:
1 K562 cells that interacted for 10min
processed data file: Counts_NK92.csv


title: Brain, SSDS, ventral hippocampus, rep2

description:
Library name: Sample 8
Column name in raw_All_Samples.txt: TBG_GFP_2

value: SSDS


title: C1498_45deg_5h_5

description: Library name: Cell_ID_69


title: K562_59_p5_6min_JH00010_S65251

description:
1 K562 cells that interacted for 6min
processed data file: Counts_NK92.csv


title: Brain, SSDS, ventral hippocampus, rep1

description:
Library name: Sample 7
Column name in raw_All_Samples.txt: TBG_GFP_1


title: Patient AC-001-104 CLL treatment-naïve PD-1-

description: Library name: 3_AC-001-104-PD-1neg_S28

value: Peripheral Blood

value: CLL cell


title: C1498_45deg_5h_4

description: Library name: Cell_ID_68


title: Patient AC-001-069 CLL treatment-naïve PD-1-

description: Library name: 27_AC-001-069_PD-1neg_S45

value: Tumor cell


title: Brain, none, ventral hippocampus, rep3

description:
Library name: Sample 6
Column name in raw_All_Samples.txt: NC_3


title: K562_5768_p30_15min_JH00010_S65226

description:
1 K562 cells that interacted for 15min
processed data file: Counts_NK92.csv


title: K562_568_p1_2min_JH00011_S65204


title: C1498_45deg_5h_3

description: Library name: Cell_ID_67


title: Brain, none, ventral hippocampus, rep2

description:
Library name: Sample 5
Column name in raw_All_Samples.txt: NC_2


title: Patient AC-001-050 CLL treatment-naïve PD-1-

description: Library name: 24_AC-001-050_PD-1neg_S42

value: Chronic Lymphocytic Leukemia

value: del13q, trisomy 12


title: K562_5601_p29_12min_JH00010_S65227

description:
1 K562 cells that interacted for 12min
processed data file: Counts_NK92.csv


title: Patient AC-001-060 CLL treatment-naïve PD-1-

description: Library name: 21_AC-001-060_PD-1neg_S39


title: C1498_45deg_5h_2

description: Library name: Cell_ID_66


title: Brain, none, ventral hippocampus, rep1

description:
Library name: Sample 4
Column name in raw_All_Samples.txt: NC_1


title: C1498_45deg_5h_1

description: Library name: Cell_ID_65


title: Brain, SSDS, ventral hippocampus, rep3

description:
Library name: Sample 9
Column name in raw_All_Samples.txt: TBG_GFP_3


title: Patient AC-014-001 CLL treatment-naïve PD-1-

description: Library name: 18_AC-014-001_PD-1neg_S36


title: Brain, CSDS, ventral hippocampus, rep3

description:
Library name: Sample 3
Column name in raw_All_Samples.txt: CSDS_3

value: CSDS


title: K562_5322_p27_20min_JH00010_S65228

description:
1 K562 cells that interacted for 20min
processed data file: Counts_NK92.csv


title: K562_5330_p7_2min_JH0021

description:
1 K562 cells that interacted for 2min
processed data file: Counts_PrimNK.csv


title: C1498_45deg_1h_13

description: Library name: Cell_ID_64


title: Patient AC-001-066 CLL treatment-naïve PD-1-

description: Library name: 15_AC-001-066-PD-1neg_S33

value: Unmutated


title: K562_497_p1_5min_MF232

description:
1 K562 cells that interacted for 5min
processed data file: Counts_NK92.csv


title: Brain, CSDS, ventral hippocampus, rep2

description:
Library name: Sample 2
Column name in raw_All_Samples.txt: CSDS_2


title: C1498_45deg_1h_12

description: Library name: Cell_ID_63


title: Patient AC-001-026 CLL treatment-naïve PD-1-

description: Library name: 12_AC-001-026-PD-1neg_S30


title: Brain, CSDS, ventral hippocampus, rep1

description:
Library name: Sample 1
Column name in raw_All_Samples.txt: CSDS_1


title: K562_4439_p20_8min_MF247_S61490

description:
1 K562 cells that interacted for 8min
processed data file: Counts_NK92.csv


title: C1498_45deg_1h_11

description: Library name: Cell_ID_62


title: Patient AC-001-051 CLL treatment-naïve PD-1+

description: Library name: 7_AC-001-051-PD-1hi_S25


title: K562_4217_p35_15min_JH00011_S65213


title: Patient AC-001-105 CLL treatment-naïve PD-1+

description: Library name: 4_AC-001-105-PD-1hi_S22


title: K562_4188_single_0min_JH0021

description:
1 K562 cells that did not interact
processed data file: Counts_PrimNK.csv


title: C1498_45deg_1h_9

description: Library name: Cell_ID_60


title: Replicate 2: A549 ells were infected with A/WSN/1933 (H1N1) (WSN) virus. Collected at 9hpi

city: Hong Kong

first: Honglin

last: Chen

state: Hong Kong

address: L501, 5/F, Lab Block, 21 Sassoon Road, Pokfulam, HK

department: Microbiology

country: Hong Kong

institute: The University of Hong Kong

description:
Library name: s9_2
Enrichment of poly A mRNA for DRS sequencing

data_processing:
Dorado latest version
Raw reads were basecalled using Dorado to assess read quality (parameters: -- estimate-poly-a).
Pass reads were mapped to genome using minimap2(parameters: -ax splice -uf)
Read count extraction and normalization were performed using salmon
Assembly: hg38, A/WSN/1933 (H1N1) (WSN) genome
Supplementary files format and content: *m6A_information.txt
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: A549 cell line

growth_protocol: A549 cells were cultured in DMEM with 10% Fetal Bovine Serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin at 37oC in a 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using Quick-RNA Miniprep (Zymo). 30 µg of totall RNA were used for sequencing library construction.
Prepared mRNA was used for DRS library construction following the Oxford Nanopore DRS protocol (SQK-RNA004, Oxford Nanopore Technologies).

treatment_protocol: Cells were infected with A/WSN/1933 (H1N1) (WSN) virus at an MOI=2, then collected cells at 3 and 9 hours post infection.

value: A549 cell line

value: human lung epithelial cells

tag: virus strain

tag: collection time

value: 9 hours post infection


title: Replicate 3: A549 ells were infected with A/WSN/1933 (H1N1) (WSN) virus. Collected at 9hpi

description:
Library name: s9_3
Enrichment of poly A mRNA for DRS sequencing

tag: cell type


title: Patient AC-001-107 CLL treatment-naïve PD-1+

description: Library name: 28_AC-001-107_PD-1hi_S46

value: Normal


title: Replicate 1: A549 ells were infected with A/WSN/1933 (H1N1) (WSN) virus. Collected at 9hpi

description:
Library name: s9_1
Enrichment of poly A mRNA for DRS sequencing


title: C1498_45deg_1h_8

description: Library name: Cell_ID_59


title: Patient AC-001-069 CLL treatment-naïve PD-1+

description: Library name: 25_AC-001-069_PD-1hi_S43

value: Mutated


title: Patient AC-001-050 CLL treatment-naïve PD-1+

description: Library name: 22_AC-001-050_PD-1hi_S40


title: K562_3941_t6_c2_5min_JH00014_S65156

value: K562 cells

tag: number of cells

value: WT


title: K562_392_p2_3min_JH00011_S65206

description:
1 K562 cells that interacted for 3min
processed data file: Counts_NK92.csv

tag: interaction duration


title: Replicate 2: A549 ells were infected with A/WSN/1933 (H1N1) (WSN) virus. Collected at 3hpi

description:
Library name: s3_2
Enrichment of poly A mRNA for DRS sequencing

value: 3 hours post infection


title: C1498_45deg_1h_6

description: Library name: Cell_ID_57


title: C1498_45deg_1h_7

description: Library name: Cell_ID_58


title: C1498_45deg_1h_5

description: Library name: Cell_ID_56


title: Patient AC-001-060 CLL treatment-naïve PD-1+

description: Library name: 19_AC-001-060_PD-1hi_S37

value: treatment-naïve

value: Trisomy 12


title: Replicate 1: A549 ells were infected with A/WSN/1933 (H1N1) (WSN) virus. Collected at 3hpi

description:
Library name: s3_1
Enrichment of poly A mRNA for DRS sequencing


title: C1498_45deg_1h_4

description: Library name: Cell_ID_55


title: E63_mG_high [RNA-Seq]

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: 10x Genomics single cell multiome (RNA)

data_processing:
Raw reads were aligned to the improved pig genome and pre-processed using the 10x Genomics CellRangerARC pipeline (v 2.0.0) for downstream analyses.
Assembly: ensembl sus scrofa v101
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Sus scrofa

source_name: Pancreas

extract_protocol:
Freshly dissected pancreata were minced into fine pieces and digested with collagenase V (0.5 mg/mL for E20-50, 1 mg/mL for E60-85, Sigma-Aldrich) for 5 mins followed by dissociation with TrypLE™ Express (Gibco) for 10-15 mins at 37°C. Cell suspension was filtered through a 40 µm cell strainer, and stained with EpCAM antibody in 1% BSA + PBS (1:200, Invitrogen) for 30 mins at 4°C. Cells were then washed and filtered into a tube through a 35 µm filter. 7-AAD (Invitrogen) was used to distinguish dead cells. The resulting cell suspension was loaded onto a FACSAria III (BD) for sorting. GFP+/7-AAD-/EpCAM+ pancreatic epithelial cells were enriched.
For nuclei isolation and library construction, a low input nuclei isolation protocol adapted from 10X Genomics was performed. In brief, sorted cells were washed once with 1 mL PBS + 1% BSA, counted, centrifuged, and supernatant was aspirated. Subsequently, the washed cell pellet was resuspended in chilled lysis buffer with 0.5x detergent concentration (50 μL per sample) and placed on ice for 5 min. Then wash buffer (500 μL per sample) was added and nuclei were centrifuged. To gradually change from wash to diluted nuclei buffer, cells were washed once in a 1:1 mixture of wash buffer and diluted nuclei buffer and subsequently one with pure diluted nuclei buffer. The washed isolated nuclei were then resuspended in 7-10 μl diluted nuclei buffer and were directly added to the transposition reaction after quality control and counting. In all following steps, 10X Genomics’ Single Cell Multiome ATAC and gene-expression protocols were followed according to the manufacturer’s specifications and guidelines.

value: Pancreas

tag: age

tag: enrichment

value: EpCAM/mG


title: Patient AC-001-066 CLL treatment-naïve PD-1+

description: Library name: 13_AC-001-066-PD-1hi_S31

value: Peripheral Blood

value: CLL cell

value: Tumor cell

value: del13q, del11q


title: Patient AC-014-001 CLL treatment-naïve PD-1+

description: Library name: 16_AC-014-001_PD-1hi_S34

value: Chronic Lymphocytic Leukemia


title: C1498_45deg_1h_10

description: Library name: Cell_ID_61


title: C1498_45deg_1h_3

description: Library name: Cell_ID_54


title: K562_386_t2_c1_5min_JH00014_S65126

tag: experiment id

tag: genotype

tag: phenotype


title: Patient AC-001-026 CLL treatment-naïve PD-1+

description: Library name: 10_AC-001-026-PD-1hi_S28

tag: tissue

tag: treatment


title: K562_4077_p24_20min_JH00010_S65258


title: E63_mG_low [ATAC-Seq]

description: 10x Genomics single cell multiome (ATAC)

library_source: genomic

molecule: genomic DNA


title: K562_3727_p4_22min_JH0018

description:
1 K562 cells that interacted for 22min
processed data file: Counts_PrimNK.csv

value: GFP


title: Replicate 3: A549 ells were infected with A/WSN/1933 (H1N1) (WSN) virus. Collected at 3hpi

description:
Library name: s3_3
Enrichment of poly A mRNA for DRS sequencing

tag: cell line

value: A549 cell line

value: human lung epithelial cells


title: E63_mG_low [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)


title: K562_3919_p33_20min_JH00011_S65219


title: E85_mG_low [ATAC-Seq]


title: Panc-1 PDS IP BG4 Rep B

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

country: Italy

institute: University of Udine

description:
Library name: RG6
rG4 enrichment in PDS treated cells

data_processing:
Basecalls performed using the FastQC/MultiQC programs
Raw reads were clipped from their adapter sequences using the Trimmomatic software (v0.35). Reads with an average Phred quality lower than 28 and length < 36 bp were discarded
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version version 2.3.5.1 with default configuration for paired reads
SAM files filtered using samtools to filter out reads with mapping quality < 10
Duplicate reads were flagged using samtools but no duplicates were removed
Peaks were called using MACS2 version 2.2.9.1  in its paired-end  analysis mode ('-f BAMPE')
Assembly: GRCh38 (Ensembl 107)
Supplementary files format and content: Coverage tracks were generated using the bamCoverage (deepTools) tool, taking an alignment of reads as input (BAM file) and generating a coverage track (bigWig) as output, applying the following parameters: --outFileFormat bigwig --binSize 50 -p 10 --normalizeUsing RPKM
Supplementary files format and content: BigWig, narrowPeak (except for Input samples)

source_name: Pancreatic ductal adenocarcinoma

growth_protocol: Cells were grown in DMEM (Euroclone, Italy) supplemented with 10 % FBS, penicillin/streptomycin and 2 mM L-glutamine (Euroclone, Italy) at 37 °C, 5 % CO2. 1µM Pyridostatin was used where indicated (PDS SML2690, Sigma-Aldrich, Germany),

extract_protocol:
30 x 10^6 Panc-1 cells, treated or not for 16 h with 1 µM PDS, were collected and then lysed for 10 min. with Hypotonic Lysis buffer (5 mM Pipes, 85 mM KCl, 0.5 % NP40) containing protease inhibitor cocktail. Pellets containing nuclei were discarded while cytoplasmic fraction was diluted 1:1 in G4RP buffer (150 mM KCl, 25 mM Tris pH 7.4, 5 mM EDTA, 0.5 mM DTT and 0.5 % NP40 in nuclease-free water). After preclearing, lysates were incubated with  3 μg of BG4 (Merck) antibody and 8 μl Dynabeads Protein G for 6h at 4°C. After washings, beads were incubated with 1ml of Tri-Reagent (Sigma-Aldrich, Germany) to extract RNA with a phenol/chloroform extraction method. RNA was DNAseI (Thermo Fisher Scientific) treated to digest genomic DNA. Concentration, integrity and purity of RNA were checked using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit).
10 ng of RNA was digested with DNAseI (NEB), freed from rRNA (using the ribo-zero method) and reverse transcribed to obtain cDNA. Adapters were ligated to the fragmented cDNA after end repair and A-tailing according to  Illumina protocols. 16 rounds of PCR amplification were performed to enrich the cDNA fragments. The PCR products were then purified using Ampure XP beads (Agencourt) and subjected to paired-end 100 sequencing at the Genewiz Genomics facility (Genewiz, Germany).

value: Pancreatic ductal adenocarcinoma

value: PDAC

value: diploid

value: PDS 1µM


title: K562_3640_p8_13_5min_JH0020

description:
1 K562 cells that interacted for 13.5min
processed data file: Counts_PrimNK.csv

value: K562 cells

value: WT


title: C1498_45deg_-1h_6

description: Library name: Cell_ID_51


title: E85_mG_low [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)


title: E63_mG_high [ATAC-Seq]


title: K562_39_p25_30min_JH00013_S65175

description:
1 K562 cells that interacted for 30min
processed data file: Counts_NK92.csv


title: K562_3639_p30_15min_JH00011_S65217

description:
1 K562 cells that interacted for 15min
processed data file: Counts_NK92.csv


title: C1498_45deg_-1h_5

description: Library name: Cell_ID_50


title: Panc-1 input Rep B

description:
Library name: RG4
Reference for rG4 enrichment

treatment_protocol: 1µM Pyridostatin was used where indicated (PDS SML2690, Sigma-Aldrich, Germany),


title: E85_mT&mG_high [ATAC-Seq]


title: K562_3636_p10_30min_MF232


title: C1498_45deg_-1h_4

description: Library name: Cell_ID_49


title: E85_mT&mG_high [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)


title: K562_363_p8_15min_MF224


title: Panc-1 PDS IP BG4 Rep A

description:
Library name: RG3
rG4 enrichment in PDS treated cells


title: C1498_45deg_-1h_3

description: Library name: Cell_ID_48


title: Panc-1 untreated IP BG4 Rep A

description:
Library name: RG2
rG4 enrichment in untreated cells

value: Unt


title: C1498_45deg_1h_2

description: Library name: Cell_ID_53


title: E45_mG [ATAC-Seq]

value: Pancreas


title: Patient AC-001-104 CLL treatment-naïve PD-1+

description: Library name: 1_AC-001-104-PD-1hi_S19

tag: cell

tag: condition

value: treatment-naïve

tag: disease

value: del13q, trisomy 12

value: Mutated


title: C1498_45deg_-1h_2

description: Library name: Cell_ID_47


title: K562_3611_p7_15_5min_JH0020

description:
1 K562 cells that interacted for 15.5min
processed data file: Counts_PrimNK.csv


title: Panc-1 input Rep A

description:
Library name: RG1
Reference for rG4 enrichment


title: E45_mG [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)

value: EpCAM/mG


title: C1498_45deg_1h_1

description: Library name: Cell_ID_52


title: K562_3688_single_0min_JH0018

description:
1 K562 cells that did not interact
processed data file: Counts_PrimNK.csv


title: K562_3473_single_0min_JH0017


title: Panc-1 untreated IP BG4 Rep B

description:
Library name: RG5
rG4 enrichment in untreated cells


title: C1498_45deg_-1h_1

description: Library name: Cell_ID_46


title: E45_mT [ATAC-Seq]

value: EpCAM/mT


title: AdrenocorticalTumor_ACME_scFASTseq_1

city: Moscow

first: Valentin

last: Trofimov

address: Ulyanova str.11

country: Russia

institute: Endocrinology Research Center

description: SeekGene

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the SeekSoulTools software v1.2.1.  (http://seeksoul.seekgene.com/en/v1.2.1/index.html)
Assembly: Genome assembly GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: adrenocortical tumor

extract_protocol:
Single cells were isolated from tissue samples using ACME HS followed by cryopreservation in 3xSSC*10% DMSO and methanol cell fixation. Key adaptations of the ACME HS method were the supplement of solution composition with 0.1M NAC and the introduction of additional washing steps in cold high salt 3xSSC* buffer. ACME dissociation was conducted in ~ 1 hours on a rotator at room temperature, with periodic pipetting of the solution. Afterward, we removed the ACME solution and washed the pellet with a two-step washing in cold 3xSSC.
Single cells were captured, barcoded, and cDNA libraries were generated using the V1.1-SeekOne DD Single Cell Full-length RNA Sequence Transcriptome-seq Kit. 10,000 cells in cold 3xSSC* were mixed with RT-PCR master mix and immediately loaded together with scFAST-seq Barcoded Beads and Carrier Oil into a Chip S3. The cDNA libraries were quantified using the Qubit dsDNA HS assay kit (Thermo Fisher Scientific), and the fragment sizes were assessed with the Agilent 5200 Fragment Analyzer using a DNA HS (1-6000NT) kit. The final library was sequenced on an Illumina Novaseq 6000 platform using the S4 Reagent Kit v1.5 (200 cycles).

value: adrenocortical tumor

value: ACME HS dissociation


title: AsPC1 CDX tumor, IK-595-treated, 48 hours after last IK-595 dose, rep4

city: Boston

first: Alexander

last: Ivliev

state: MA

address: 645 Summer Street, Suite 101

institute: Ikena Oncology, Inc.

data_processing:
Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Quality of fastq files was assessed using fastqc software (v0.12.1).
Counts and transcript per million (TPM) were generated from fastq files using Salmon (v0.14.1) with the “validateMappings”, “gcBias”, and “seqBias” flags on. Salmon index was based on GENCODE human transcriptome (Release 38, GRCh38.p13) with the entire human genome sequence used as decoy.
Tximport R package (1.28.0) was used to collect counts and TPM values across samples into respective matrices.
Assembly: GENCODE human transcriptome (Release 38, GRCh38.p13)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes transcripts per million (TPM) for each Sample

source_name: tumor tissue

extract_protocol:
RNA extraction, library preparation, sequencing, and analysis was conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as described below.  Total RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal micro kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).  The sequencing libraries were clustered on a flowcell. After clustering, the flowcell was loaded on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: AsPC-1 tumor-bearing mice were treated with three doses of vehicle or IK-595 (at 6 mg/kg), by mouth, QOD. Tumors from the drug-treated mice were collected and profiled at the following time points after the last dose: 2 hours, 4 hours, 8 hours, 24 hours, and 48 hours (four animals per time point group) - to understand longitudinal gene expression changes after dosing.

value: tumor tissue

value: AsPC-1 cell line-derived xenograft

tag: treatment details

value: three rounds of treatment, 6 mg/kg, per os, QOD

tag: time

value: 48 hours after last vehicle dose


title: C1498_37deg_15h_11

description: Library name: Cell_ID_45


title: E45_mT [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)


title: K562_3298_t4_c2_4min_JH00014_S65152

description:
1 K562 cells that interacted for 5min
processed data file: Counts_NK92.csv


title: C1498_37deg_15h_10

description: Library name: Cell_ID_44


title: AsPC1 CDX tumor, IK-595-treated, 48 hours after last IK-595 dose, rep3

value: Pancreatic ductal adenocarcinoma


title: E85_GFP-_2

description: 10x Genomics

data_processing:
FASTQ files were aligned to the improved pig genome and pre-processed using the CellRanger 10x Genomics software for downstream analyses.
Assembly: ensembl v101
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Freshly dissected pancreata were minced into fine pieces and digested with collagenase V (0.5 mg/mL for E20-50, 1 mg/mL for E60-85, Sigma-Aldrich) for 5 mins followed by dissociation with TrypLE™ Express (Gibco) for 10-15 mins at 37°C. Cell suspension was filtered through a 40 µm cell strainer, and stained with EpCAM antibody in 1% BSA + PBS (1:200, Invitrogen) for 30 mins at 4°C. Cells were then washed and filtered into a tube through a 35 µm filter. 7-AAD (Invitrogen) was used to distinguish dead cells. The resulting cell suspension was loaded onto a FACSAria III (BD) for sorting. 7-AAD-/EpCAM+ cells from pancreata were collected and pancreata of INS-eGFP embryos at specified ages were used to enrich eGFP+/7-AAD-/EpCAM+ endocrine cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, SC-islet cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: INS-eGFP

value: EpCAM/GFP


title: K562_3254_t5_c2_5min_JH00014_S65150

value: K562 cells

value: WT


title: C1498_37deg_15h_9

description: Library name: Cell_ID_43


title: E85_GFP+_2

description: 10x Genomics

value: Pancreas


title: C1498_37deg_15h_8

description: Library name: Cell_ID_42


title: K562_3192_p2_2min_JH00013_S65190

description:
1 K562 cells that interacted for 2min
processed data file: Counts_NK92.csv


title: E85_GFP-_1

description: 10x Genomics


title: E85_GFP+_1

description: 10x Genomics


title: K562_3164_p25_20min_JH00011_S65222

description:
1 K562 cells that interacted for 20min
processed data file: Counts_NK92.csv


title: AsPC1 CDX tumor, IK-595-treated, 24 hours after last IK-595 dose, rep4

value: 24 hours after last vehicle dose


title: C1498_37deg_15h_7

description: Library name: Cell_ID_41


title: K562_31083_p2_10min_JH0017

description:
1 K562 cells that interacted for 10min
processed data file: Counts_PrimNK.csv

value: GFP


title: AsPC1 CDX tumor, IK-595-treated, 24 hours after last IK-595 dose, rep3


title: E85_WT_2

description: 10x Genomics

value: Wild-type

value: EpCAM


title: K562_306_p27_40min_JH00013_S65176

description:
1 K562 cells that interacted for 40min
processed data file: Counts_NK92.csv


title: C1498_37deg_15h_6

description: Library name: Cell_ID_40


title: K562_3320_p14_15min_JH00010_S65257


title: AsPC1 CDX tumor, IK-595-treated, 24 hours after last IK-595 dose, rep2


title: E85_WT_1

description: 10x Genomics


title: C1498_37deg_15h_4

description: Library name: Cell_ID_38


title: K562_3059_p5_2min_JH00013_S65189


title: C1498_37deg_15h_5

description: Library name: Cell_ID_39


title: AsPC1 CDX tumor, IK-595-treated, 24 hours after last IK-595 dose, rep1


title: C1498_37deg_15h_3

description: Library name: Cell_ID_37


title: K562_3037_single_0min_JH0020


title: E63_6_GFP-

description: 10x Genomics


title: AsPC1 CDX tumor, IK-595-treated, 8 hours after last IK-595 dose, rep4

value: 8 hours after last vehicle dose


title: WT_E63_3

description: 10x Genomics


title: C1498_37deg_15h_2

description: Library name: Cell_ID_36


title: AsPC1 CDX tumor, IK-595-treated, 48 hours after last IK-595 dose, rep1


title: AsPC1 CDX tumor, IK-595-treated, 48 hours after last IK-595 dose, rep2


title: AsPC1 CDX tumor, IK-595-treated, 8 hours after last IK-595 dose, rep3


title: K562_2956_p8_2min_JH00013_S65188


title: C1498_37deg_15h_1

description: Library name: Cell_ID_35


title: K562_292_p4_2min_JH00011_S65214


title: K562_28832_p5_15min_JH0017

description:
1 K562 cells that interacted for 15min
processed data file: Counts_PrimNK.csv


title: AsPC1 CDX tumor, IK-595-treated, 8 hours after last IK-595 dose, rep2


title: WT_E63_2

description: 10x Genomics


title: AsPC1 CDX tumor, IK-595-treated, 8 hours after last IK-595 dose, rep1


title: C1498_37deg_10h_6

description: Library name: Cell_ID_34


title: E23_2

description: 10x Genomics


title: C1498_37deg_10h_5

description: Library name: Cell_ID_33


title: AsPC1 CDX tumor, IK-595-treated, 4 hours after last IK-595 dose, rep4

value: 4 hours after last vehicle dose


title: E23_1

description: 10x Genomics


title: K562_2776_p2_7min_MF247_S61485

description:
1 K562 cells that interacted for 7min
processed data file: Counts_NK92.csv


title: K562_2710_p21_15min_JH00011_S65220


title: C1498_37deg_10h_4

description: Library name: Cell_ID_32


title: E54_3

description: 10x Genomics


title: AsPC1 CDX tumor, IK-595-treated, 4 hours after last IK-595 dose, rep3


title: E54_2

description: 10x Genomics


title: K562_2678_p6_4min_JH0020

description:
1 K562 cells that interacted for 4min
processed data file: Counts_PrimNK.csv


title: K562_2509_p16_10min_JH00011_S65223

description:
1 K562 cells that interacted for 10min
processed data file: Counts_NK92.csv


title: AsPC1 CDX tumor, IK-595-treated, 4 hours after last IK-595 dose, rep1


title: AsPC1 CDX tumor, IK-595-treated, 4 hours after last IK-595 dose, rep2


title: C1498_37deg_10h_2

description: Library name: Cell_ID_30


title: K562_2444_p15_10min_JH00011_S65221


title: E63_4_GFP+

description: 10x Genomics


title: C1498_37deg_10h_1

description: Library name: Cell_ID_29


title: AsPC1 CDX tumor, IK-595-treated, 2 hours after last IK-595 dose, rep4

value: 2 hours after last vehicle dose


title: E54_1

description: 10x Genomics


title: PIP male flea 1

city: Seville

first: Angela

middle: M.

last: García Sánchez

address: Profesor García González, 2

country: Spain

institute: Universidad de Sevilla

description: Library name: Sample PIP.m.1

data_processing:
Paired-end reads were merged using FLASH V1.2.7
Quality filtering on the raw tags was performed according to QIIME V1.9
Chimeric merged reads were detected and removed using UCHIME
Multiple sequence alignment was conducted using MUSCLE V 3.8.31
Assembly: NCBI genome assembly ASM342690v1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Pulex irritans

extract_protocol:
Total DNA was extracted from fleas using flea abdomen by the DNeasy Blood  and Tissue Kit (Qiagen, Valencia, CA, U.S.A.) in accordance with the manufacturer’s instructions
Sequencing libraries were generated using TruSeq DNA PCR- Free Sample Preparation Kit (Illumina, USA) following manufacturer's recommendations

tag: host

value: Dog

tag: gender

value: Male


title: K562_2328_single_0min_JH0020

tag: cell type

tag: number of cells


title: C1498_37deg_5h_6

description: Library name: Cell_ID_28


title: AsPC1 CDX tumor, IK-595-treated, 2 hours after last IK-595 dose, rep3

value: tumor tissue

value: AsPC-1 cell line-derived xenograft

value: three rounds of treatment, 6 mg/kg, per os, QOD


title: PIP female flea 2

description: Library name: Sample PIP.f.2

value: Female


title: K562_2327_p5_2_5min_JH0021

description:
1 K562 cells that interacted for 2.5min
processed data file: Counts_PrimNK.csv

tag: interaction duration


title: C1498_37deg_5h_5

description: Library name: Cell_ID_27


title: PIP female flea 1

description: Library name: Sample PIP.f.1


title: K562_2309_p2_22min_JH0018

description:
1 K562 cells that interacted for 22min
processed data file: Counts_PrimNK.csv


title: AsPC1 CDX tumor, IK-595-treated, 2 hours after last IK-595 dose, rep1

value: Pancreatic ductal adenocarcinoma


title: C1498_37deg_10h_3

description: Library name: Cell_ID_31


title: C1498_37deg_5h_4

description: Library name: Cell_ID_26


title: C1498_37deg_5h_3

description: Library name: Cell_ID_25


title: C. albicans tetO-YSF3/Δ, 37°C YPD, - DOX, rep3

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

institute: Freie Universität

description: Library name: Ca_ysf3_37_n_r3

data_processing:
Paired-end RNA-seq data were trimmed with cutadapt/2.10 to remove any residual adaptor sequences using the following flags and settings: cutadapt --cores=0 -b CTGTCTCTTATACACATCT -B CTGTCTCTTATACACATCT -e 0.1 -O 10 -m 16 --output=R1t.fastq.gz --paired-output=R2t.fastq.gz $R1 $R2 (Martin, 2011).
Trimmed data were mapped to the Candida albicans SC5314 genome, version A22 with HISAT version 2.2.1 using the following command: hisat2 --summary-file summary.txt --max-intronlen 2000 -x C_albicans_SC5314_A22 --rna-strandness FR -1 $R1 -2 $R2 -S out.sam --novel-splicesite-outfile novelSS.txt (Kim et al., 2015).
Using samtools, bedtools and igvtools (SAMtools/1.9, BEDTools/2.27.1, igvtools 2.14.1), hisat2 output was further filtered to retain only mapped reads and converted into bam- and coverage-files (tdf and bedgraph) for visualization in IGV and downstream analyses (Li et al., 2009; Quinlan and Hall, 2010; Thorvaldsdóttir et al., 2013).
Assembly: Candida albicans SC5314 genome, version A22
Supplementary files format and content: TDF File (read coverage)
Supplementary files format and content: Text File (read counts per gene)

organism: Candida albicans

growth_protocol: Liquid cultures were grown in YPD at 30°C, YPD plates were maintained at 4°C 1 month max.

extract_protocol:
Cell pellets were flash frozen, lysed by bead beating, followed by RNA extraction using the RNAeasy kit (Qiagen) and DNase treatment using the DNA-free DNA removal kit (Invitrogen).
Sample libraries were prepared using the Illumina Stranded mRNA Ligation Kit and sequenced with the Illumina Novaseq 6000 using a 150bp paired-end protocol and multiplexing to obtain >50 million paired-end reads/sample.

treatment_protocol: Overnight cultures were grown in YPD with and without 0.05 µg/ml DOX shaking, and sub-cultured to an OD of 0.2 in 10 ml YPD with and without 20 µg/ml DOX and grown for four hours at respective temperature before harvesting cells for RNA extraction

value: 37°C - DOX


title: K562_2282_p3_5min_MF232

value: K562 cells

value: WT


title: K562_2294_p4_5min_JH0021

description:
1 K562 cells that interacted for 5min
processed data file: Counts_PrimNK.csv


title: K562_2219_p12_5min_JH00013_S65185


title: C. albicans tetO-YSF3/Δ, 37°C YPD, - DOX, rep2

description: Library name: Ca_ysf3_37_n_r2

value: 37°C -DOX


title: AsPC1 CDX tumor, vehicle-treated, 2 hours after last vehicle dose, rep3

value: vehicle (5% DMSO/95% PEG400)

value: three rounds of treatment, per os, QOD


title: AsPC1 CDX tumor, vehicle-treated, 2 hours after last vehicle dose, rep4


title: C1498_37deg_5h_2

description: Library name: Cell_ID_24


title: C. albicans tetO-YSF3/Δ, 37°C YPD, - DOX, rep1

description: Library name: Ca_ysf3_37_n_r1


title: K562_2212_p5_2min_JH0020

description:
1 K562 cells that interacted for 2min
processed data file: Counts_PrimNK.csv

value: GFP


title: C1498_37deg_1h_11

description: Library name: Cell_ID_22


title: AsPC1 CDX tumor, vehicle-treated, 2 hours after last vehicle dose, rep1


title: C. albicans tetO-YSF3/Δ, 37°C YPD, + DOX, rep2

description: Library name: Ca_ysf3_37_d_r2

value: 37°C + DOX


title: C. albicans tetO-YSF3/Δ, 37°C YPD, + DOX, rep3

description: Library name: Ca_ysf3_37_d_r3


title: C1498_37deg_1h_10

description: Library name: Cell_ID_21


title: C1498_37deg_5h_1

description: Library name: Cell_ID_23


title: C. albicans tetO-YSF3/Δ, 37°C YPD, + DOX, rep1

description: Library name: Ca_ysf3_37_d_r1


title: AsPC1 CDX tumor, IK-595-treated, 2 hours after last IK-595 dose, rep2


title: K562_2162_p17_10min_JH00011_S65218


title: K562_2146_p10_4min_JH00013_S65187

description:
1 K562 cells that interacted for 4min
processed data file: Counts_NK92.csv


title: C1498_37deg_1h_9

description: Library name: Cell_ID_20


title: CD composite 1

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

data_processing:
*library strategy: spatial transcriptomics
Reads were subjected to Spaceranger 2.1.1 pipeline
Assembly: hg38
Supplementary files format and content: OSR_IBD_1_A1.filtered_feature_bc_matrix.h5: Spaceranger filtered binary matrix
Supplementary files format and content: OSR_IBD_2_B2.filtered_feature_bc_matrix.h5: Spaceranger filtered binary matrix

source_name: Ileums

extract_protocol:
Libraries were made according to the 10x Genomics Visium Spatial Gene Expression - FFPE Library Construction kit
240 bp paired-end

value: Ileums


title: C. albicans tetO-YSF3/Δ, 22°C YPD, - DOX, rep3

description: Library name: Ca_ysf3_22_n_r3

value: 22°C - DOX


title: C1498_37deg_1h_8

description: Library name: Cell_ID_19


title: C. albicans tetO-YSF3/Δ, 22°C YPD, - DOX, rep2

description: Library name: Ca_ysf3_22_n_r2


title: CD composite 2


title: K562_21_p4_12_5min_JH0020

description:
1 K562 cells that interacted for 12.5min
processed data file: Counts_PrimNK.csv


title: AsPC1 CDX tumor, vehicle-treated, 2 hours after last vehicle dose, rep2

value: 2 hours after last vehicle dose


title: C1498_37deg_1h_7

description: Library name: Cell_ID_18


title: OLAPARIB+RT 2

city: Ann Arbor

first: Qiang

last: Zhang

state: Michigan

address: 1500 E Medical Center Dr

department: Radiation Oncology

institute: University of Michigan

description: Sample 11

data_processing:
Sequence reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure quality of data
Fastq Screen v was used to screen for contamination
Reads were mapped to GRch38 (ENSEMBL) using STAR v2.7.8a
Assigned count estimates to genes with RSEM v1.3.3
Alignment following ENCODE standards for RNA-seq
Multiqc v1.7compiled the results from these tools to provide quality control report
Assembly: GRch38
Supplementary files format and content: tab de-limited text file includes raw counts for each sample
Supplementary files format and content: tab de-limited text file includes FPKM for each sample
Supplementary files format and content: tab de-limited text file includes TPM for each sample

growth_protocol: BT245 cells were were cultured in the tumor stem media (TSM) basic medium supplied with B27 minus vitamin A (Thermo Fisher, #12587010), human recombinant EGF (PeproTech, #AF-100-15), human recombinant bFGF (PeproTech, #100-18B), human recombinant PDGF-AA (PeproTech, #100-13A), human recombinant PDGF-BB (PeproTech, #100-14B), and Heparin (Stem Cell Technologies, #07980).

extract_protocol:
Total mRNAs were extracted using RNeasy Mini Kit (Qiagen) and treated with DNase digestion (Qiagen) following manufecture's instructions
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files

treatment_protocol: BT245 cells treated with olaparib (3 µM, 1 hr pre-RT) and/or RT (8 Gy) were harvested at 72 h post-RT.

value: Diffuse midline glioma

value: Mutation:H3.3K27M; TP53 R117S

value: OLAPARIB+RT


title: C1498_37deg_1h_6

description: Library name: Cell_ID_17


title: K562_2094_p11_5min_JH00013_S65186


title: C. albicans tetO-YSF3/Δ, 22°C YPD, - DOX, rep1

description: Library name: Ca_ysf3_22_n_r1


title: K562_2118_t2_c2_5min_JH00014_S65125


title: C1498_37deg_1h_5

description: Library name: Cell_ID_16


title: C. albicans tetO-YSF3/Δ, 22°C YPD, + DOX, rep3

description: Library name: Ca_ysf3_22_d_r3

value: 22°C + DOX


title: RT 3

description: Sample 9

value: RT


title: K562_2042_p9_10min_JH00010_S65254


title: OLAPARIB+RT 3

description: Sample 12


title: C. albicans tetO-YSF3/Δ, 22°C YPD, + DOX, rep2

description: Library name: Ca_ysf3_22_d_r2


title: C1498_37deg_1h_4

description: Library name: Cell_ID_15


title: K562_2003_p12_9min_MF247_S61489

description:
1 K562 cells that interacted for 9min
processed data file: Counts_NK92.csv


title: C. albicans tetO-YSF3/Δ, 22°C YPD, + DOX, rep1

description: Library name: Ca_ysf3_22_d_r1


title: RT 1

description: Sample 7


title: C1498_37deg_1h_3

description: Library name: Cell_ID_14


title: RT 2

description: Sample 8


title: K562_1972_t6_c1_5min_JH00014_S65155


title: K562_1934_p9_4min_MF247_S61486


title: C1498_37deg_1h_2

description: Library name: Cell_ID_13


title: OLAPARIB 3

description: Sample 6

value: OLAPARIB


title: C. albicans WT, 37°C YPD, - DOX, rep2

description: Library name: Ca_WT_37_n_r2

value: wild-type


title: C1498_37deg_1h_1

description: Library name: Cell_ID_12


title: OLAPARIB+RT 1

description: Sample 10


title: K562_1894_p10_10min_JH0021

value: K562 cells


title: K562_1693_p3_22min_JH0018

value: WT


title: OLAPARIB 2

description: Sample 5


title: C. albicans WT, 37°C YPD, - DOX, rep1

description: Library name: Ca_WT_37_n_r1

value: 37°C -DOX


title: C1498_37deg_-1h_11

description: Library name: Cell_ID_11


title: K562_1648_p2_10_5min_JH0020

description:
1 K562 cells that interacted for 10.5min
processed data file: Counts_PrimNK.csv


title: C1498_37deg_-1h_10

description: Library name: Cell_ID_10


title: C. albicans WT, 37°C YPD, + DOX, rep3

description: Library name: Ca_WT_37_d_r3


title: CONTROL 3

description: Sample 3

value: CONTROL


title: C1498_37deg_-1h_9

description: Library name: Cell_ID_9


title: C. albicans WT, 37°C YPD, + DOX, rep2

description: Library name: Ca_WT_37_d_r2

value: 37°C +DOX


title: K562_1630_p15_9min_JH00013_S65184


title: OLAPARIB 1

description: Sample 4


title: CONTROL 2

description: Sample 2


title: C. albicans WT, 37°C YPD, + DOX, rep1

description: Library name: Ca_WT_37_d_r1


title: K562_1573_p10_6min_MF247_S61491

description:
1 K562 cells that interacted for 6min
processed data file: Counts_NK92.csv


title: C. albicans WT, 37°C YPD, - DOX, rep3

description: Library name: Ca_WT_37_n_r3

value: 37°C - DOX


title: CONTROL 1

description: Sample 1


title: C1498_37deg_-1h_8

description: Library name: Cell_ID_8


title: K562_15551_p4_8min_JH0017

description:
1 K562 cells that interacted for 8min
processed data file: Counts_PrimNK.csv

value: GFP


title: C1498_37deg_-1h_7

description: Library name: Cell_ID_7


title: hPSC Pancreatic Endocrine Progenitor Monolayer, NEUROG3 AF3444, ChIP, Rep 3, Batch 3

city: Cincinnati

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
ChIP-seq read were aligned to UCSC hg19 genome using Bowtie2.
Peaks were called using HOMER2 using significant cutoff q-value<0.05
Assembly: hg19
Supplementary files format and content: bigWig

source_name: hPSC-derived Pancreatic Endocrine Progenitor Monolayer

extract_protocol:
Collected samples were cross-linked in 1% formaldehyde in PBS for 12 min at room temperature and was stopped by replacing with 0.125 M glycine. Nuclei was pelleted in lysis buffer. The desired amount of fragmented chromatin was supplemented with Nuclear Lysis Dilution Buffer and precleared with blocked Protein G magnetic beads (Thermo Fisher Scientific) with rotation at 4 oC for 3 h. 1% precleared samples were saved as input and each 25μg sample was incubated with 20μg Protein G magnetic beads preloaded with 5ug antibody overnight with rotation at 4 oC. Beads were then washed sequentially at 4 oC. Protein-DNA complexes were eluted from the beads in Elution Buffer (50 mM Tris-HCl pH=8, 10 mM EDTA, 1% SDS) at 65°C for 30min. Cross-links were reversed at 65°C overnight, and DNA was purified with phenol:chloroform, chloroform and ethanol for library construction
ChIP-seq libraries was prepared and sequenced at CCHMC DNA sequencing and Genotyping Core Facility. DNA libraries were prepared using 5-10 ng of starting material using the SMARTer ThruPLEX DNA-Seq kit (Takara; R400674). After library amplification, DNA was purified using AMPure XP beads (Beckman-Coulter; A63880) and size-selected. DNA fragment traces were analyzed on a Bioanalyzer.

value: WA01 hESC:NEUROG3-/- ; NEUROG3-TetON

value: Endocrine Progenitors Day9

tag: chip antibody

value: human NEUROG3, R&DAF3444

value: 8-hour Dox


title: C. albicans WT, 22°C YPD, - DOX, rep2

description: Library name: Ca_WT_22_n_r2

value: 22°C - DOX


title: hPSC Pancreatic Endocrine Progenitor Monolayer, NEUROG3 AF3444, ChIP, Rep 2, Batch 2

value: hPSC-derived Pancreatic Endocrine Progenitor Monolayer


title: K562_1497_p16_10min_JH00013_S65183

tag: experiment id


title: C. albicans WT, 22°C YPD, - DOX, rep1

description: Library name: Ca_WT_22_n_r1

tag: genotype


title: K562_1494_p1_18min_JH0021

description:
1 K562 cells that interacted for 18min
processed data file: Counts_PrimNK.csv

tag: phenotype


title: C1498_37deg_-1h_5

description: Library name: Cell_ID_5


title: hPSC Pancreatic Endocrine Progenitor Monolayer, NEUROG3 AF3444, ChIP, Rep 1, Batch 1

tag: tissue


title: K562_1493_p17_9min_JH00013_S65179

tag: treatment


title: C1498_37deg_-1h_4

description: Library name: Cell_ID_4

tag: cell line


title: C. albicans WT, 22°C YPD, + DOX, rep3

description: Library name: Ca_WT_22_d_r3

value: 22°C + DOX


title: K562_1443_p6_10min_MF232


title: C. albicans WT, 22°C YPD, - DOX, rep3

description: Library name: Ca_WT_22_n_r3


title: K562_13_p6_5min_JH00010_S65252

description:
1 K562 cells that interacted for 5min
processed data file: Counts_NK92.csv


title: C1498_37deg_-1h_2

description: Library name: Cell_ID_2


title: VE6_EC

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
The read qualities for each fastq file were accessed with FastQC (V 0.11.9), and low-quality bases and adapters were removed with Trimmomatic.
The sequenced reads were mapped to the bovine reference genome (bosTau 9) with the STAR aligner (V 2.7.0b), generating the genome index with the ARS-UCD1.3 assembly.
Read counts were estimated at the gene level, and the counting was done with featureCounts, part of the Subread software (V 2.0.3).
Assembly: bosTau 9
Supplementary files format and content: tab delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: ED

extract_protocol:
Embryo samples were shipped in dry ice to the BGI TECH SOLUTIONS Company (Hong Kong), which performed the RNA extraction, quality control, library preparation and sequencing.
RNA sequencing (RNAseq) was run in the RNA samples through non-stranded & polyA-selected mRNA library preparation and PE100 sequencing with 5Gb clean data per sample on DNBSEQ. After library preparation and sequencing, raw data with adapter sequences or low-quality sequences were filtered to remove contamination and obtain valid data. This step was completed by the SOAPnuke software developed by BGI Company.

treatment_protocol: For IVP embryos, oocytes aspirated from slaughterhouse ovaries were matured, fertilized, and cultivated in serum-free medium until transfer at day 7. IVV embryos (n=8) were generated after ovarian super-stimulation and artificial insemination. For both procedures, animals were flushed at day 15 of gestation, and sections of the ED and EEM were snap-frozen in 0,1% PVA PBS until shipment.

value: ED

tag: developmental stage

value: Day 15 elongated embryo

value: IVV


title: WT, 100, 8h, 72hpi_, Rep2

description: PW108722_CRRA200015679-1a_H5MMTDSXY_L3_1

data_processing:
Read mapping, raw count and tpm were generated using CSBB-v2.0
Assembly: hg19
Supplementary files format and content: tab-delimited text files including counts per sample
Supplementary files format and content: tab-delimited text files including TPM per sample

extract_protocol:
Samples were collected on differentiation days 9, 10, 11 and 12 with or without 8-hour NEUROG3 induction. All RNA samples were column purified using a NucleoSpin RNA kit (Machery-Nagel) including an on-column DNAse digestion. Frozen RNA samples were sent for library construction
Library construction and sequencing was performed by Novogene

value: NEUROG3-/- ; NEUROG3-TetON

value: Endocrine progenitors day 12


title: C1498_37deg_-1h_6

description: Library name: Cell_ID_6


title: VE5_T1C

source_name: EEM

value: EEM

tag: condition


title: C1498_37deg_-1h_3

description: Library name: Cell_ID_3


title: WT, 100, 8h, 72hpi, Rep3

description: PW108723_CRRA200015680-1a_H5MMTDSXY_L3_1


title: K562_1278_t5_c1_5min_JH00014_S65149

data_processing:
Raw reads were trimmed using trimmomatic (version 0.32)
aligned to the mouse reference genome (mm10) using HISAT2 (version 2.1.0)
Uniquely mapped reads for each exon were counted using the function summarizeOverlaps from the Ge-nomicAlignments package (version 1.12.0) in R (version 3.4.0)
Gene and exon annotations were obtained from the Ensembl GENCODE Basic set (genome-build GRCh38)
Assembly: hg38
Supplementary files format and content: csv file of read counts

extract_protocol:
RNA was isolated according to Smart-seq2 was performed as described previously (Picelli et.  al., 2014). In brief, cells were lysed in 0.2% Triton X-100 in the presence of RNase inhibitor 40 U/µl RNase inhibitor (Takara) and stored at -80°C until ready to proceed.
RNA was denatured, reverse transcribed and amplified for 22 cycles. After reverse transcription, 1 ng cDNA was tagmented, amplified and barcoded following the Illumina Nextera indexing strategy. Final libraries were pooled to 4 nM for sequencing on HiSeq3000/4000. cDNA and library quality was assessed using TapeStation 4150 instrument and D5000HS or D1000 screening tapes (Agilent), respectively. DNA concentration was determined using Qubit dsDNA HS kit and instrument (Invitrogen). cDNA and Illumina Nextera indexed samples were purified using Ampure XP beads (Beckman Coulter) at 1:1 ratio. Sequencing was performed by the Biomedical Sequencing Facility at CeMM at 50bp single-end configuration.

value: K562 cells

value: WT


title: C1498_37deg_-1h_1

description: Library name: Cell_ID_1

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Each library was sequenced twice, and the generated fastq files were merged for each library.
Reads were aligned to the mm10 genome assembly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Assembly: Mouse mm10
Supplementary files format and content: The calculated copy number of RNA moelcules per cell for each gene is listed.

extract_protocol:
RNAs from cell lysate was directly used for library preparation.
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.


title: IL-17 positive cells 27-01

city: Hannover

first: Ziqing

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

description: Library name: IL17-pos-27-01-delta

data_processing:
Sequencing reads from obtained FASTQ files were aligned and annotated with MiXCR according to the international immunogenetics information system. Annotated files were analyzed with V(D)J tools and the Immunarch package in R.
Assembly: mm10
Supplementary files format and content: the variable (V), diversity (D), and joining (J) segments used in the TCR delta chains in specific contexts.

source_name: peripheral lymphnode

extract_protocol:
TCR amplicon generation and NGS RNA was extracted from FACS-sorted  IL-17pos and IL-17neg γδ T cells from pLNs of Vγ4-/- / Vγ6-/- mice, using an RNeasy Micro Kit (Qiagen).
For TRD (TRDV1 and TRDV5) repertoire analysis, the isolated mRNA was reverse-transcribed using SMARTer RACE 5’-3’ PCR Kit (Clontech) with a customized protocol. Next, the CDR3 region of TRD clones was amplified via RACE PCR.

value: peripheral lymphnode

tag: strain

value: gamma delta T cells

value: IL-17 positive cells

value: PMA stimulation on pLN cells


title: WT, 100, 8h, 72hpi, Rep1

description: PW108721_CRRA200015678-2a_H5NVTDSXY_L1_1


title: C. albicans WT, 22°C YPD, + DOX, rep1

description: Library name: Ca_WT_22_d_r1

value: wild-type


title: K562_1196_p21_15min_JH00013_S65182

city: Vienna

first: Jakob

address: Zimmermannpl. 10

institute: Children’s Cancer Research Institute

description:
1 K562 cells that interacted for 15min
processed data file: Counts_NK92.csv


title: VE4_T1C


title: hPSC Pancreatic Endocrine Progenitor Monolayer, Input, Batch 1

value: WA01 hESC:NEUROG3-/- ; NEUROG3-TetON

value: Endocrine Progenitors Day9

value: 8-hour Dox


title: K562_1132_t3_c1_5min_JH00014_S65128


title: C. albicans WT, 22°C YPD, + DOX, rep2

description: Library name: Ca_WT_22_d_r2

value: 22°C + DOX


title: WT, 100, 8h, 48hpi, Rep1

description: PW108481_CRRA200015672-1a_H5MMTDSXY_L3_1

value: hPSC-derived Pancreatic Endocrine Progenitor Monolayer

value: Endocrine progenitors day 11


title: VE4_EC

value: ED

value: Day 15 elongated embryo

value: IVV


title: IL-17 positive cells 13-01

description: Library name: IL17-pos-13-01-delta


title: K562_1101_p8_4min_JH00011_S65210


title: WT, 100, 8h, 48hpi, Rep2

description: PW108482_CRRA200015673-1a_H5MMTDSXY_L3_1

value: NEUROG3-/- ; NEUROG3-TetON


title: IL-17 negative cells 27-01

description: Library name: IL17-neg-27-01-delta

value: IL-17 negative cells


title: VE3_T1A

value: EEM


title: K562_1234_p7_5min_JH00011_S65216

value: K562 cells


title: WT, 100, 8h, 24hpi, Rep3

description: PW108243_CRRA200015668-1a_H5MMTDSXY_L2_1

value: Endocrine progenitors day 10


title: WT, 100, 8h, 24hpi, Rep2

description: PW108242_CRRA200015667-1a_H5MMTDSXY_L2_1


title: WT, 100, 8h, 24hpi, Rep1

description: PW108241_CRRA200015666-1a_H5MMTDSXY_L2_1


title: VE29_T1C


title: IL-17 negative cells 20-01

description: Library name: IL17-neg-20-01-delta

value: peripheral lymphnode

value: gamma delta T cells


title: WT, 100, 8h, 48hpi, Rep3

description: PW108483_CRRA200015674-1a_H5MMTDSXY_L3_1


title: K562_1034_p11_12min_MF239_S61508

description:
1 K562 cells that interacted for 12min
processed data file: Counts_NK92.csv


title: K562_110_p1_5min_MF224

value: WT


title: K562_10229_p3_6min_JH0017

description:
1 K562 cells that interacted for 6min
processed data file: Counts_PrimNK.csv

value: GFP


title: VE3_EA


title: VE5_EC


title: WT, 100, 8h, 8hpi, Rep3

description: PW108083_CRRA200015662-1a_H5MMTDSXY_L2_1

value: Endocrine progenitors day 9


title: IL-17 positive cells 20-01

description: Library name: IL17-pos-20-01-delta

value: IL-17 positive cells

value: PMA stimulation on pLN cells


title: WXJ

city: Guangzhou

first: Xiaoqiang

last: YANG

address: 12,Jichang Road

institute: Guangzhou University of Chinese Medicine

description:
Library name: sample4
10X Genomics

data_processing:
Sequencing data were processed using Cell Ranger (10x Genomics) for quality control, filtering, and normalization. Low-quality cells and genes were excluded from analysis. Dimensionality reduction was performed using principal component analysis (PCA), followed by clustering using Louvain algorithms, and visualized using t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) to identify distinct cell populations. Differential gene expression analysis was conducted to identify key marker genes for cell types and subpopulations. Cell-cell communication was analyzed using tools like CellPhoneDB.
Assembly: human NCBI genome build 36
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tissue cell

extract_protocol:
Single cells were sorted from the suspension using flow cytometry to remove debris and dead cells. The single-cell suspension was loaded onto the 10x Genomics Chromium platform for encapsulation in microfluidic droplets, where each droplet contained a single cell and reagents for reverse transcription. Cell-specific barcodes and unique molecular identifiers (UMIs) were incorporated during cDNA synthesis. After reverse transcription, cDNA was amplified and prepared for sequencing through library construction. The libraries were then sequenced using an Illumina platform to generate high-throughput single-cell RNA sequencing data.
The Chromium™ Single Cell 3' Solution is built on the GemCode technology microfluidics platform, which encapsulates gel beads with barcodes and primers along with individual cells in oil droplets to form GEMs (Gel Bead in Emulsion). GEM refers to the mixture of oil droplets containing barcoded Gel beads and cells, along with reaction reagents. The primers are composed of the full-length Illumina TruSeq Read 1 sequencing primer, a 16bp 10X Barcode sequence (used for cell identification), a 12bp unique molecular identifier (UMI) (used to distinguish different transcripts from the same cell and to remove PCR duplicates), and a 30 bp poly dT reverse transcription primer.The prepared cell suspension, 10X Barcode gel beads, and oil droplets are separately introduced into different channels (a total of 8 channels) of the Chromium Next GEM Chip G. The GEMs (Gel Bead in Emulsion) are formed through a microfluidic system. To achieve a single-cell reaction system, the concentration of the cell suspension is controlled between 700-1200 cells per microliter (µl). As a result, 90-99% of the GEMs do not contain any cells, while the majority of the remaining GEMs contain a single cell.Within the GEM (Gel Bead in Emulsion), the gel beads dissolve, and the cells lyse to release mRNA.  This mRNA is then reverse transcribed to produce barcoded cDNA for sequencing.  The liquid oil layer is disrupted, and cDNA amplification is carried out.  After purification, quality control is performed, and once the quality is confirmed, library construction is initiated.Enzymatic cutting is performed, followed by end-repairing of the fragments and the addition of an A-base overhang. Adapters are then ligated. The target-sized fragments are recovered using a size-selection kit, and the library is subjected to quality control and quantification.The constructed library structure, from 5' to 3', consists of: Illumina P5 adapter, P5 sequencing primer (black Read1 position), 16bp Barcode, 12bp Unique Molecular Identifier (UMI), poly(dT) random nucleotide (VN) sequence, inserted cDNA fragment, P7 sequencing primer (black Read2 position), sample Index (i7 index read), and Illumina P7 adapter. The可用 (yòng, which means 'available' or 'usable' in this context) sequence length for Read 1 is 28 base pairs (bp) (16bp Barcode + 12bp UMI), which is used to distinguish between cells and the different transcripts (mRNA) within each cell. The可用 (yòng) sequence length for Read 2 is 91 base pairs (bp), which is used to map to a reference genome to determine gene information.

value: cystic change

tag: disease state

value: SIONFH


title: IL-17 negative cells 13-01

description: Library name: IL17-neg-13-01-delta


title: VE29_EC

value: ED


title: WT, 100, 8h, 8hpi, Rep2

description: PW108082_CRRA200015661-1a_H5MMTDSXY_L2_1

value: hPSC-derived Pancreatic Endocrine Progenitor Monolayer

value: 8-hour Dox


title: K562_10181_t3_c2_5min_JH00014_S65127

last: Huemer


title: VE28_T1C

value: Day 15 elongated embryo

value: IVV


title: Jurkat_8487_single_0min_JH0024

description:
1 Jurkat cells that did not interact
processed data file: Counts_CAR.csv

source_name: Jurkat cells

value: Jurkat cells


title: WT, 100, 8h, 8hpi, Rep1

description: PW108081_CRRA200015660-1a_H5MMTDSXY_L2_1

value: NEUROG3-/- ; NEUROG3-TetON


title: bone_cyst

description:
Library name: sample2
10X Genomics


title: VE28_EC


title: Jurkat_6729_single_0min_JH0024


title: KO, 0, 8h, 72hpi, Rep3

description: PW008723_CRRA200015677-1a_H5MMTDSXY_L3_1

value: Endocrine progenitors day 12

value: no Dox


title: AL_bone_cyst

description:
Library name: sample1
10X Genomics


title: VE26_T1C

value: EEM


title: Jurkat_5222_p11_15min_JH0024

description:
1 Jurkat cells that interacted for 15min
processed data file: Counts_CAR.csv

value: WT


title: KO, 0, 8h, 72hpi, Rep2

description: PW008722_CRRA200015676-1a_H5MMTDSXY_L3_1


title: Muscle_AI_Female_4

city: Dublin

first: Laura

last: Thompson

address: Belfield

country: Ireland

institute: University College Dublin

description:
Library name: Sample_32
Muscle_16

source_name: Calf muscle

extract_protocol:
Blood and tissues samples were shipped on dry ice to Macrogen Europe (Amsterdam, Netherlands), which performed the RNA extraction, quality control, library preparation, and sequencing.
Libraries were prepared with Truseq-stranded mRNA for all tissue samples and SMARTer Stranded RNA library for the blood samples, followed by PE100 sequencing with the NovaSeq platform, generating ~30 million raw reads per sample in FASQ format.

value: Calf muscle

tag: Sex

value: Female

value: AI

tag: age at_biopsy

value: 121 days


title: VE26_EC


title: DWR

description:
Library name: sample3
10X Genomics

value: cystic change


title: Muscle_AI_Female_3

description:
Library name: Sample_31
Muscle_15

value: 130 days


title: KO, 0, 8h, 72hpi, Rep1

description: PW008721_CRRA200015675-1a_H5MMTDSXY_L3_1


title: VE24_EC

value: ED


title: Jurkat_4196_p9_10min_JH0024

description:
1 Jurkat cells that interacted for 10min
processed data file: Counts_CAR.csv

value: GFP


title: Muscle_AI_Female_2

description:
Library name: Sample_30
Muscle_14

value: 138 days


title: Jurkat_4680_p4_19min_JH0028

description:
1 Jurkat cells that interacted for 19min
processed data file: Counts_CAR.csv


title: KO, 0, 8h, 48hpi, Rep3

description: PW008483_CRRA200015671-1a_H5MMTDSXY_L3_1

value: hPSC-derived Pancreatic Endocrine Progenitor Monolayer

value: Endocrine progenitors day 11


title: VE19_T1A

value: Day 15 elongated embryo

value: IVV


title: VE24_T1C


title: Muscle_AI_Female_1

description:
Library name: Sample_29
Muscle_13

value: 142 days


title: KO, 0, 8h, 48hpi, Rep2

description: PW008482_CRRA200015670-1a_H5MMTDSXY_L3_1

value: NEUROG3-/- ; NEUROG3-TetON

value: no Dox


title: Jurkat_4

description:
500 Jurkat cells that did not interact
processed data file: Counts_CAR.csv

value: Jurkat cells

value: WT


title: VE19_EA


title: Muscle_IVP_Female_4

description:
Library name: Sample_28
Muscle_12

value: Calf muscle

value: Female

value: IVP

value: 118 days


title: Jurkat_3991_p9_14min_JH0028

description:
1 Jurkat cells that interacted for 14min
processed data file: Counts_CAR.csv


title: KO, 0, 8h, 48hpi, Rep1

description: PW008481_CRRA200015669-1a_H5MMTDSXY_L3_1


title: Muscle_IVP_Female_3

description:
Library name: Sample_27
Muscle_11

value: 120 days


title: KO, 0, 8h, 24hpi, Rep3

description: PW008243_CRRA200015665-1a_H5MMTDSXY_L2_1

value: Endocrine progenitors day 10


title: IVPF9_T1A

value: EEM


title: Jurkat_3671_p8_14_5min_JH0028

description:
1 Jurkat cells that interacted for 14.5min
processed data file: Counts_CAR.csv

value: GFP


title: Muscle_IVP_Female_2

description:
Library name: Sample_26
Muscle_10

value: 130 days


title: IVPF15_EC

value: ED


title: KO, 0, 8h, 24hpi, Rep2

description: PW008242_CRRA200015664-1a_H5MMTDSXY_L2_1

value: hPSC-derived Pancreatic Endocrine Progenitor Monolayer


title: Jurkat_3188_p3_4_5min_JH0028

description:
1 Jurkat cells that interacted for 4.5min
processed data file: Counts_CAR.csv


title: Muscle_IVP_Female_1

description:
Library name: Sample_25
Muscle_9

value: 143 days


title: Jurkat_5051_p10_14_5min_JH0024


title: KO, 0, 8h, 24hpi, Rep1

description: PW008241_CRRA200015663-1a_H5MMTDSXY_L2_1


title: IVPF14_TA

value: Day 15 elongated embryo


title: Jurkat_3073_p1_4_5min_JH0028


title: KO, 0, 8h, 8hpi, Rep3

description: PW008083_CRRA200015659-1a_H5MMTDSXY_L2_1

value: NEUROG3-/- ; NEUROG3-TetON

value: Endocrine progenitors day 9


title: IVPF14_EA


title: Jurkat_3

value: Jurkat cells


title: Muscle_AI_Male_3

description:
Library name: Sample_23
Muscle_7

value: Male

value: AI

value: 133 days


title: IVPF13_T1A

value: IVP


title: KO,0, 8h, 8hpi, Rep1

description: PW008081_CRRA200015657-1a_H5MMTDSXY_L2_1

value: no Dox


title: Muscle_AI_Male_2

description:
Library name: Sample_22
Muscle_6

value: Calf muscle

value: 136 days


title: Muscle_AI_Male_4

description:
Library name: Sample_24
Muscle_8

value: 114 days


title: IVPF13_EA


title: KO, 0, 8h, 8hpi, Rep2

description: PW008082_CRRA200015658-1a_H5MMTDSXY_L2_1


title: Jurkat_2255_p10_9min_JH0028

description:
1 Jurkat cells that interacted for 9min
processed data file: Counts_CAR.csv

value: WT

value: GFP


title: Muscle_AI_Male_1

description:
Library name: Sample_21
Muscle_5


title: P2_hiPSCs with trisomy 21-derived cardiac cells

first: Juli

last: Liu

state: Guangdong

address: Zhongshan 2nd road

department: Medical Research Center

institute: Guangdong provincial people's hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by trimming reads containing adapter, ploy-N or with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were performed based on the clean data with high quality.
Index of the reference genome was built using hisat2-2.0.4 and paired-end clean reads were mapped to the reference genome. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads. Stringtie-1.3.3b was used to count the read numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of at least two biological replicates per group was performed by using the edgeR_3.24.3. Genes with an adjusted P-value <0.05 were assigned as differentially expressed genes (DEGs).
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: EXCEL files include read counts for each Sample

source_name: hiPSC-cardiac cells

growth_protocol: All hiPSCs were cultured in mTesR1 medium. All hiPSCs were differentiated towards cardiac cells by using STEMdiff cardiomyocyte differentiation kit (Stem cell tech.) according to the manual

extract_protocol:
total RNAs were harvested using RNeasy Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations

value: hiPSC-cardiac cells

value: trisomy 21


title: IVPF10_EC

value: ED


title: Jurkat_2


title: Muscle_IVP_Male_4

description:
Library name: Sample_20
Muscle_4

value: 117 days


title: Jurkat_2261_p11_9min_JH0028


title: Jurkat_1834_p14_14min_JH0028


title: P1_hiPSCs with trisomy 21-derived cardiac cells


title: N2_isogenic normal hiPSC-derived cardiac cells

value: normal


title: IVP14_EC

value: Day 15 elongated embryo


title: IVP14_T1C

value: EEM


title: Jurkat_1767_p13_9_5min_JH0028

description:
1 Jurkat cells that interacted for 9.5min
processed data file: Counts_CAR.csv

value: Jurkat cells


title: Muscle_IVP_Male_2

description:
Library name: Sample_18
Muscle_2

value: Male

value: 137 days


title: N1_isogenic normal hiPSC-derived cardiac cells


title: IVP11_T1C

value: IVP


title: Muscle_IVP_Male_1

description:
Library name: Sample_17
Muscle_1

value: 143 days


title: Jurkat_1307_p5_18min_JH0028

description:
1 Jurkat cells that interacted for 18min
processed data file: Counts_CAR.csv


title: Jurkat_128_p2_4_5min_JH0028


title: 47_ChIPseq_shNCOR_H3K27ac_rp1

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

description: Library name: Sample 47

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Supplementary files format and content: The differential expression file was further provided(tab-delimited file).
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
RNA-seq raw files (fastq, PE150) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.

source_name: monocyte

growth_protocol:
WT RAW264.7 cells, lentivirus-medicated knockdown cells were maintained normal 10% FBS DMEM medium.
RAW264.7 cells  with lentivirus-medicated knockdown cells were maintained normal 10% FBS DMEM medium.
RAW264.7  cells were maintained normal 10% FBS DMEM medium.
shGFP, shNCOR and shSMRT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
Fresh cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) for 30 minutes, followed by 1% formaldehyde for 10 minutes at room temperature. Nuclei were isolated, sonicated, and incubated with magnetic bead-antibody complexes.  Antibodies to NCOR (bethyl, A301-145A), SMRT (bethyl, A301-147A), and GPS2 (homemade) were used.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×105 cells one day before the experiments. Cells were washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
2×105 shGFP, shNCOR and shSMRT cells were seeded one day before the treatment. Total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
105 shGFP, shNCOR and shSMRT cells were seeded one day before the treatment. Total RNA was extracted from the manufacturer's introduction.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol:
No treatment
No treatment
No treatment
RAW264.7 cells were treated with or without LPS (100ng/ml), IL4 (20ng/ml), GW3965 (5uM) for 3 hours. H3K27ac (Abcam, ab4729) was used for the Cut&Tag experiment.

value: monocyte

value: Macrophages

value: BALB/c

tag: batch

value: ChIP-seq


title: Liver_AI_Female_3

description:
Library name: Sample_15
Liver_15

source_name: Calf liver

value: Calf liver

value: Female

value: AI

value: 130 days


title: IVP10_T1C


title: 46_ChIPseq_shGFP_n_H3K27ac_rp2

description: Library name: Sample 46

tag: cell type


title: IVP10_EC

value: ED


title: 45_ChIPseq_shGFP_n_H3K27ac_rp1

description: Library name: Sample 45


title: Jurkat_1

tag: number of cells

value: WT

value: GFP


title: Liver_AI_Female_2

description:
Library name: Sample_14
Liver_14

value: 138 days


title: Liver_AI_Female_1

description:
Library name: Sample_13
Liver_13

value: 142 days


title: Muscle_IVP_Male_3

description:
Library name: Sample_19
Muscle_3

value: Calf muscle

value: Male

value: 136 days


title: Day10_EC_Cd31po_Rnf20_het_r2

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
High quality trimmed reads were mapped to the mm10 reference genome using STAR (v. 2.7.10a) (−alignIntronMin 20 −alignIntronMax 500000) (Dobin et al., 2013).
Mapped sam files were used to create makeTaglibraries using makeTagDirectory (default settings).
analyzeRepeats.pl function (rna mm10 -strand both -count genes –noadj) from HOMER (Heinz et al., 2010) was used to quantify the mapped reads.
Differential expression was quantified and normalized by Deseq2 (v. 1.40.1). rpkm.default (defaults) from EdgeR (v. 3.42.4) was used to calculate the reads per kilobase of million reads (RPKM).
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150).
Assembly: mm10 from UCSC genome
Supplementary files format and content: BigWig files
Supplementary files format and content: Excel file from differential expression analysis.

source_name: ESC derived Endothelial cells

growth_protocol: E14 Tg(Nkx2–5-EmGFP) ES cells were differentiated according to Rui et al. 2018 and at day3.7 cells were differentiated towards EC. At day10, cells were selected by CD31 positive cells for RNA extraction.

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen.
Hieff NGS C102P1 Ultima Dual-mode mRNA.

treatment_protocol: ES differentiation protocol according to (https://doi.org/10.1038/s41422-019-0168-1).

value: ESC derived Endothelial cells

value: CRISPR _CAS9_Rnf20

value: sorted positive CD31 cells


title: Day10_EC_Cd31po_Rnf20_het_r1


title: 43_ChIPseq_shSMRT_H3K27ac_rp1

description: Library name: Sample 43

value: monocyte

value: Macrophages

value: BALB/c


title: Day10_EC_Cd31po_Rnf20_Ctr_r2

value: Ctr


title: Jurkat_1450_single_0min_JH0028

description:
1 Jurkat cells that did not interact
processed data file: Counts_CAR.csv

value: Jurkat cells

tag: interaction duration