title: ATN_pos_8, No-rejection, DSA-positive

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

data_processing:
High throughput sequencing of the final pool was performed using the NovaSeq6000 S4 system (Illumina) with the following instrument settings: paired-end, 150 b, 300–400 million reads per lane.
Raw data were automatically processed by Basespace cloud interface (Illumina) in default settings. The basecalling, adapter clipping, and quality filtering were carried out using bcl2fastq v2.20.0.422 Conversion Software (Illumina).
The quality of raw reads was evaluated using FastQC (v0.11.5) and MultiQC (v1.6).
Clipping adaptor sequences was carried out using cutadapt (v1.18). The trimmed reads were aligned to the human cDNA reference (GeCh38) using bowtie2 (v 2.1.0). The counts of reads mapped to the reference were extracted and used for differential gene expression analysis using SAMtools (v1.2).
DESeq2 R library version 4.2.2 was applied to normalize read counts and to identify differences in gene expression between sample groups
Assembly: human transcriptome reference (GeCh38)
Supplementary files format and content: Matrix table with raw transcript counts for every transcript and every sample

source_name: kidney transplant biopsy

extract_protocol:
Total RNA was isolated from kidney tissue using Trizol-chloroform extraction, concentration was measured by Qubit fluorimetr and RNA integrity number was checked using Agilent Bioanalyzer 2100. From 400 ng of total RNA, mRNA was isolated using poly (A) magnetic selection NEBNext® Poly (A) mRNA magnetic isolation module (New England, BioLabs, Inc).
Transcriptome libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads according to the manufacturer’s protocol (New England, BioLabs, Inc).In brief, mRNA was randomly fragmented by heat digestion in the presence of a divalent metal cation (Mg2+). Sheared RNA was reversibly transcribed making 1st strand of cDNA using random hexamers as primers and reverse transcriptase. The second strand was created using dUTPs, purified with NEBNext Sample Purification Beads, and ligated with diluted NEBNext adapters. After removal of the 2nd strand by uracil-DNA-dependent glycosylase, the final amplification of adaptor-ligated DNA was done using NEBNext® Multiplex Oligos for Illumina®.
Library was purified with NEBNext Sample Purification Beads and its quality was assessed on a Bioanalyzer 2100 using the Agilent DNA 1000 assay.

value: kidney transplant biopsy

value: No-rejection

tag: time from_transplantation_(days)

tag: donor specific_antibodies

value: Yes


title: ATN_pos_7, No-rejection, DSA-positive

status: Public on Dec 26 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: ATN_pos_6, No-rejection, DSA-positive


title: VR-0637

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

country: USA

institute: Ichan School of Medicine at Mount Sinai

data_processing:
The raw RNA sequencing data was aligned to human genome hg38 using STAR 2.5.3a with default parameters and the expression of each gene was quantified with HTseq count with default parameters.
Assembly: hg38
Supplementary files format and content: Raw count expression matrix.

source_name: Whole blood

extract_protocol: Total RNA was isolated from the whole blood stored in PAXgene tubes and then subjected to standard RNA sequencing libraries generation by following manufacturer protocol.

value: Whole blood

tag: ethnicity

value: Not Hispanic or Latino

tag: race

value: European

tag: treatment

value: Pre-transplant


title: 8 pooled cell lines, Multi-Seq

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Department of Biochemistry and Biophysics

institute: UCSF

description:
Library name: pooled_ars1620 multidose_HTO
multi-seq library with barcode x treatment assignments

library_source: other

data_processing:
Raw single-cell FASTQ files were used as input into the 10X Cell Ranger pipeline with default parameters. Briefly, reads were aligned to the hg38 transcriptome using STAR generating a filtered feature-barcode matrix and bam alignment file.
Pooled scRNA-Seq experiments were demultiplexed into individual cell lines using Demuxlet with the CB tag, setting the fixed mixing proportion, alpha, to 0.5. Demultiplexing of single cell barcodes into drug treatments using hashtag oligos (HTOs) was performed using pymulti from the scEasyMode python library (https://github.com/johnnyUCSF/scEasyMode) , Multiplexed scRNA-Seq count matrices were processed using scanpy. Counts were normalized (normalize_per_cell) and, log-transformed (log1p). Additionally, droplets predicted as doublets by demuxlet were removed. Normalized count matrices were used to calculate PCA, leiden clusters, and UMAP representations.
Assembly: hg38 cellranger reference
Supplementary files format and content: cellranger counts outputs of different lanes in h5 format
Supplementary files format and content: processed anndata objects with cell line and drug treatment calls

molecule: other

growth_protocol: Cell lines were grown in RPMI complete, 10% FBS with 1X Pen-strep. Cells were seeded in 6 well plates at 50k/well for a T0 time point. After 72 hours, cells were harvested by trypsin and counted to arrive at total cell numbers. Growth rates were calculated by the following formula: r = ln(Y t/Y 0)/t. Cell line pooling for GENEVA was performed by harvesting all cell lines simultaneously by trypsin digestion, washing in 1X PBS, counting, and inversely balancing against growth rate. Cells were seeded at specific numbers inverse to the growth rate into a single sterile tube and then mixed well before plating into separate wells in vitro, or injections into different mice for flank xenograft studies. All cell line pooling was performed in less than 2 hours total time to ensure healthy cell pools.

extract_protocol:
ells were prepared for single-cell RNA sequencing by trypsin digestion for 10 minutes at 37C when harvested from in-vitro culture. For harvest of organoids and in-vivo xenograft tumors, cells were harvested by resection, chopping with a razor blade into a slurry, and then resuspension in 1 mg/mL Liberase TM. Suspensions were incubated shaking at 37C at 150 RPM for 45 minutes after which cells were resuspended in ACK buffer and incubated at room temperature for 10 minutes. Resuspension in 1X PBS was performed two times following this for wash and removal of digestion buffers. Cells were passed through a 70 micron mesh filter to arrive at single-cell suspensions.
Cell suspensions were then hashed using HTO oligos or Totalseq-A antibodies. Cell suspensions were assigned unique oligo-HTO or antibody-HTOs at the point of experimentation. Cells were incubated with corresponding HTO conjugate for 20 minutes on ice. Cells were then washed 3X in 1X cold PBS and then recounted. Cells were then pooled together from multiple hashed suspensions such that there were equivalent numbers of cells from each suspension prior to 10X single-cell preparation. All single-cell studies were hashed in this way..
GENEVA libraries were prepared according to single-cell RNA sequencing Chromium kit instructions. Modifications were performed after the cDNA step in which the small fractions were harvested and then amplified in separate PCR reactions for enrichment of the hashtag reads, also as specified in Chromium kit. Sequencing was performed for the transcriptome and hashtag libraries at a 95%/5% ratio (transcriptome/hashtag). Sequencing targets were 25,000 reads/cell based on expected cell counts determined by number of cells loaded at input into the chromium kit.

treatment_protocol: In vitro compound treatments were prepared by diluting the compound to final concentration in 1X RPMI complete, 10%FBS, pen-strep with no more than 1% DMSO in the final solution. Combination treatments were prepared in the same way. In vitro treatments received media changes with fresh compound dilutions every 48 hours. In vivo delivery was formulated as specified for the specific study and dosed by standard IP or PO dosing.

tag: cell line

tag: cell type

value: Mixed Sample (Melanoma, Melanoma, Melanoma, Pancreatic Cancer, Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC)) Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC), Melanoma, Melanoma

tag: genotype

value: mixed sample (DMSO, ARS-1620 (0.4 µM, 1.6 µM, 25 µM) )


title: ATN_pos_5, No-rejection, DSA-positive


title: VR-0636

value: African American


title: 8 pooled cell lines, GEX

description:
Library name: pooled_ars1620 multidose_gex
pooled 10x gene expresison from cell lines, cellranger outputs, demuxlet output and processed anndata included

library_source: transcriptomic single cell

source_name: Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC)) Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC), Melanoma, Melanoma


title: ATN_pos_4, No-rejection, DSA-positive


title: ATN_pos_2, No-rejection, DSA-positive


title: VR-0634


title: VR-0635


title: ATN_pos_3, No-rejection, DSA-positive


title: ATN_pos_1, No-rejection, DSA-positive


title: ATN_neg_8, No-rejection, DSA-negative

value: No


title: VR-0629


title: ATN_neg_7, No-rejection, DSA-negative


title: VR-0628


title: ATN_neg_6, No-rejection, DSA-negative


title: Duodenum_02

type: RNA

city: Richmond

first: Grayson

middle: Welch

last: Way

email: waygw@vcu.edu, waygw@outlook.com

state: Virginia

address: 1217 E Marshall Street Room 534

department: Microbiology and Immunology

institute: VCU

hyb_protocol: Samples were prepared for nCounter gene expression profiling with a custom version of the commercially available human metabolic panel following the manufacterer's recommendations (NanoString Technologies).

scan_protocol: Scanning was performed by the nCounter Digital Analyzer.

data_processing: The data were analyzed using ROSALIND® (https://rosalind.bio/), which features a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Differentially expressed genes (DEGs) were identified based on statistical significance between two groups using a cutoff criterion of P < 0.05 and |fold change (FC)| > 1.5.

label: NanoString reporter

source_name: Intestinal pinch biopsy

label_protocol: Oligonucleotide probe hybridization following the manufacturer's (NanoString Technologies) protocol.

extract_protocol: Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific, Inc, Waltham, MA, USA) following the instructions.

tag: group

value: Compensated

tag: status

tag: patientid

value: Duodenum


title: ATN_neg_5, No-rejection, DSA-negative


title: VR-0627


title: VR-0625


title: ATN_neg_4, No-rejection, DSA-negative


title: VR-0619

value: Hispanic or Latino

value: Latin American


title: VR-0639


title: VR-0624


title: VR-0620


title: VR-0618


title: ATN_neg_2, No-rejection, DSA-negative


title: VR-0613


title: ATN_like_ABMR_8, active/probable ABMR, DSA-positive

value: active/probable ABMR


title: VR-0615


title: ATN_neg_3, No-rejection, DSA-negative


title: ATN_neg_1, No-rejection, DSA-negative


title: VR-0612


title: VR-0611


title: VR-0610


title: ATN_like_ABMR_6, active/probable ABMR, DSA-positive


title: ATN_like_ABMR_7, active/probable ABMR, DSA-positive


title: VR-0608


title: VR-0602


title: ATN_like_ABMR_3, active/probable ABMR, DSA-positive


title: ATN_like_ABMR_2, active/probable ABMR, DSA-positive


title: VR-0600


title: ABMR_8, active/probable ABMR, DSA-positive


title: VR-0599


title: VR-0497


title: ABMR_7, active/probable ABMR, DSA-positive


title: ABMR_5, active/probable ABMR, DSA-positive


title: VR-0496

value: Unknown


title: VR-0494


title: ABMR_6, active/probable ABMR, DSA-positive

value: kidney transplant biopsy


title: ABMR_3, active/probable ABMR, DSA-positive


title: ABMR_4, active/probable ABMR, DSA-positive


title: ABMR_2, active/probable ABMR, DSA-positive


title: VR-0493


title: ATN_like_ABMR_5, active/probable ABMR, DSA-positive


title: VR-0489


title: VR-0486


title: ATN_like_ABMR_4, active/probable ABMR, DSA-positive


title: VR-0603


title: VR-0482


title: VR-0492


title: VR-0491


title: Gingiva, periodontitis, rep4

city: Hangzhou, Zhejiang Province

first: Sen

last: Kang

address: 166 North Qiutao Road

country: China

institute: Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.
We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version: stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version: gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis  of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include FPKM and count values for each Sample

source_name: Gingiva

extract_protocol:
Total RNA was extracted using Trizol reagent (ThermoFisher, 15596018CN) following the manufacturer's procedure.
The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, 5067-1511), high-quality RNA samples with RIN number > 7.0 were used to construct the sequencing library.

value: Gingiva


title: VR-0480

value: Asian


title: VR-0478

value: Whole blood


title: Gingiva, periodontitis, rep3


title: VR-0485


title: VR-0601


title: ATN_like_ABMR_1, active/probable ABMR, DSA-positive

value: Yes


title: Gingiva, periodontitis, rep2


title: VR-0495

value: Not Hispanic or Latino


title: VR-0474

value: Pre-transplant


title: Gingiva, periodontitis, rep1


title: Gingiva, healthy, rep5


title: ABMR_1, active/probable ABMR, DSA-positive


title: Gingiva, healthy, rep4


title: VR-0472


title: VR-0468

value: European


title: VR-0473


title: Gingiva, healthy, rep1


title: VR-0466


title: VR-0467


title: Gingiva, healthy, rep3


title: wound tissue, experiment, 50% wound healing5

city: shanghai

first: guili

last: wang

state: 上海

address: shanghai longhang road jinshan district

institute: fudan

data_processing:
The libraries were sequenced on an llumina Novaseq 26000 platform and 150 bp paired-end reads were generated. About 3000 raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then about 6000 clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq25. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
Assembly: human NCBI genome build 36
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: wound tissue

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: DFU tissue

tag: patient

value: PLCL/Fg dressing

tag: healing

value: 50% wound healing


title: wound tissue, experiment, 50% wound healing4


title: VR-0465

value: African American


title: VR-0464


title: wound tissue, experiment, 50% wound healing3


title: VR-0463


title: wound tissue, experiment, 50% wound healing2


title: VR-0462


title: wound tissue, experiment, 50% wound healing1


title: wound tissue, control, 0% wound healing5

value: 0% wound healing


title: VR-0461


title: VR-0476

value: Hispanic or Latino


title: VR-0456


title: wound tissue, control, 0% wound healing4


title: VR-0455


title: wound tissue, control, 0% wound healing3


title: wound tissue, control, 0% wound healing2


title: Gingiva, healthy, rep2


title: R_623

data_processing:
The raw sequencing data from pre- and post-transplant blood were first aligned to human genome hg38 with STAR 2.5.3a 47 and gene expression counts in each sample was quantified with HTseq both with default parameters.
Assembly: hg38
Supplementary files format and content: Expr.txt: Tab-delimited text file includes counts.

molecule: polyA RNA

extract_protocol:
The sequencing libraries of post-transplant blood in GoCAR cohort were generated by stranded polyA selection kit.
Standard RNA sequencing libraries generation by following manufacturer protocol.
Sequenced on NovaSeqXplus sequencer at 150 bp read length and an average throughput of 30M reads per sample at Cornell Genomics Core Facility.

value: LILRB3-4SNPs risk allele

value: Kidney transplantation

tag: time point

value: 3 months post-transplantation


title: VR-0451

value: Latin American


title: wound tissue, control, 0% wound healing1


title: VR-0452


title: R_653


title: VR-0453


title: VR-0454


title: R_5217


title: VR-0450

value: Unknown


title: R_587


title: VR-0449


title: VR-0445


title: R_4318


title: R_3517


title: VR-0447

value: Asian


title: R_3017

value: Whole blood


title: VR-0444


title: VR-0458


title: R_3817


title: R_2662


title: VR-0443


title: VR-0441


title: VR-0440


title: WT_In_T3p_3

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

library_source: genomic

data_processing:
Short reads mapping (Bowtie2 v2.3.4.1)
Peak calling (MACS2 v2.1.1.20160309)
Consensus peakset and raw counts were obtained using DiffBind in R.
Assembly: X. Tropcalis genome (Xenbase version 10.0
Supplementary files format and content: *_peaks.tsv files correspond to the output of peak calling with MACS2. It contains coordinates of each peak along with peak calling metrics.
Supplementary files format and content: diffbind_rawcounts_features.tsv is the result of running  DiffBind to generate a unique peakset (by merging overlapped peaks) from set of peak files from individual samples, and counting reads over the peaks.

molecule: genomic DNA

organism: Xenopus tropicalis

source_name: Intestine

growth_protocol: Intestinal samples were collected from WT, TRαKO and TRβKO  tadpoles.

extract_protocol:
Intestine chromatin DNA was extracted and IP was performed with TR antibody. After purification of ChIP-DNA, all purified DNA was used for the construction of sequencing libraries.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When tadpoles reached to stage 54, tadpoles were treated with 10nM T3 for 18 hours.

value: Intestine

value: wild type

value: T3 treatment for 18 hours


title: R_632

value: WT


title: VR-0439

value: Not Hispanic or Latino

value: European

value: Pre-transplant


title: VR-0438

value: African American


title: WT_In_T3p_2


title: VR-0437


title: VR-0432


title: WT_In_T3p_1


title: R_4838


title: R_4697


title: VR-0431


title: VR-0433


title: WT_In_T3m_3


title: R_4337


title: VR-0430


title: WT_In_T3m_1


title: R_3617


title: R_3537


title: VR-0428


title: VR-0429


title: WT_In_T3m_2


title: R_1777


title: TRbKO_In_T3p_3

value: TR{beta}KO


title: VR-0359


title: TRbKO_In_T3p_2


title: VR-0360


title: VR-0355


title: VR-0442


title: R_3497


title: VR-0357


title: VR-0354

value: Hispanic or Latino


title: R_3177


title: R_2677


title: VR-0351


title: TRbKO_In_T3p_1


title: TRbKO_In_T3m_3


title: VR-0350


title: VR-0352


title: VR-0349


title: VR-0343


title: CCCR_ncRNA-seq_4

city: Nashville

first: Hua-Chang

last: Chen

state: TN

address: 2525 West End Avenue, Suite 1100

department: Department of Biostatistics

institute: Vanderbilt University Medical Center

description:
RNA from whole cell lysate from  CC-CR cells
smallRNAseq_human_miR_KO_raw_counts.txt

data_processing:
Demultiplexing and bioinformatic analyses was performed using the TIGER pipeline (58).  Briefly, Cutadapt (v1.16) was used to trim 3′ adaptors and then trim 4 nt from both 5' and 3' end (the random-mer sequence introduced by NEXTFlex samll RNA library preparation kit) and all reads with < 16 nucleotides (nts) were removed (59).  Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.11.9)(www.bioinformatics.babraham.ac.uk/projects/fastqc).  The adaptor-trimmed reads were mapped to the hg19 genome, with additional rRNA and tRNA reference sequences, by Bowtie1 (v1.1.2) allowing only one mismatch (60).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Colon

growth_protocol: CC-CR CRC cells were obtained from the Coffey lab (Lu et al., 2017).  All cell lines were confirmed to be free of mycoplasma contamination (VenorTMGeM Mycoplasma Detection Kit, PCR-based, Sigma Aldrich Cat #MP0025).  Cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Corning) supplemented with 10% fetal bovine serum (FBS, Corning), 1% L-glutamine (200 nM, Gibco), 1% MEM nonessential amino acids (Sigma Aldrich), and 1% penicillin-streptomycin (10,000 U/mL, Gibco) in 5% CO2 at 37°C.  Cells were passaged a maximum of 8 times before discarding

extract_protocol:
Trizol extraction was completed according to manufacturers protocol.
RNA libraries were generated using the NEXTFlex Small RNA Library Preparation Kits v3 (Perkin) with the following modifications: (1) 3′- and 5′-adaptors were diluted 1:8, (2) 3′-adaptor ligations were performed overnight in multiple steps –25°C for 2 h, 20°C for 4 h and 16°C overnight, (3) following cDNA synthesis and before barcoding PCR, step F protocol was followed, and (4) PCR amplification was 20 cycles.  Following PCR amplification, individual libraries were size-selected (136–200 bp product) using Pippin Prep (Sage Sciences).  Size-selected libraries were quantified using Qubit Fluorometer.  Libraries were checked for quality and sequenced using Illumina short-read technology.  Libraries were pooled (equimolar multiplexed libraries) and sequenced (PE150) using the NovaSeq6000 (Illumina) platform at the VANTAGE Core (Vanderbilt University).

treatment_protocol: We used CRISPR/Cas9 multiplex genome engineering (Kabadi et al., 2014) to delete miR100, miR125b, or both.  Guide RNAS (gRNAs) flanking the targeted locus were designed using the Benchling CRISPR gRNA Design Tool (https://www.benchling.com/crispr).  Oligonucleotides containing gRNA sequences were first cloned into sgRNA expression vectors (Addgene #53186-53189) and then multiple gRNA cassettes were cloned into lentiviral expression vectors (pLV hUbC-Cas9-T2A-GFP; Addgene, #53190) using Golden Gate cloning technology.  Lentiviral stocks were prepared in 293T cells and used to transduce CC-CR cells.  Single GFP+ cells were sorted into 96 cell plates and expanded.  PCR amplification of genomic DNA from clonal GFP+ cells was performed using primers flanking the gRNA target sequences to identify deletion clones.

value: Colon

value: HCA-7 Derived CC-CR {delta}miR-100/miR-125b

value: Colorectal Cancer

value: RNA from Whole Cell Lysate


title: TRbKO_In_T3m_1


title: VR-0342

value: Latin American


title: VR-0358


title: VR-0341


title: R_1638

value: Kidney transplantation

value: 3 months post-transplantation


title: TRaKO_In_T3p_3

value: Intestine

value: TR{alpha}KO


title: CCCR_ncRNA-seq_3


title: VR-0340

value: Whole blood


title: VR-0337


title: VR-0336


title: TRaKO_In_T3p_1

value: T3 treatment for 18 hours


title: CCCR_ncRNA-seq_1


title: VR-0339

value: Not Hispanic or Latino


title: D84_ncRNA-seq_1

description:
RNA from whole cell lysate from ΔmiR-100/miR-125b CC-CR cells
smallRNAseq_human_miR_KO_raw_counts.txt


title: VR-0344


title: TRbKO_In_T3m_2


title: TRaKO_In_T3m_3


title: TRaKO_In_T3p_2


title: baselineLILR093

data_processing:
The raw sequencing data from pre- and post- transplant blood were first aligned to human genome hg38 with STAR 2.5.3a 49 and gene expression counts in each sample was quantified with HTseq both with default parameters.
Assembly: hg38
Supplementary files format and content: Tab delimited text format of gene-sample raw counts expression profile

extract_protocol:
Total RNA was isolated from the whole blood stored in PAXgene tubes.
Subjected to standard RNA sequencing libraries generation by following manufactory protocol.

value: No risk allele

tag: gender

value: Male

tag: self-reported race


title: D84_ncRNA-seq_3


title: D84_ncRNA-seq_4


title: baselineLILR091

value: African American


title: D82_ncRNA-seq_4


title: baselineLILR089


title: baselineLILR087

value: Female


title: baselineLILR090


title: TRaKO_In_T3m_2


title: D82_ncRNA-seq_3


title: TRaKO_In_T3m_1


title: baselineLILR085


title: baselineLILR086


title: baselineLILR084

value: LILRB3-4SNPs risk allele


title: baselineLILR095


title: D82_ncRNA-seq_1

value: Colon


title: baselineLILR081


title: C55_ncRNA-seq_4

value: HCA-7 Derived CC-CR {delta}miR-100/miR-125b


title: Salmonella-infected (S), KO, mice 02

city: Turku

first: Madhukar

last: Vedantham

address: Kiinamyllynkatu 10-D

country: Finland

institute: University of Turku

description: Library name: S02KO

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene’s in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and 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 database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38.p6, gca_000001635_8
Supplementary files format and content: .XLS file includes raw counts for each Sample
Supplementary files format and content: .XLS file includes FPKM counts for each Sample

organism: Mus musculus

source_name: Proximal colon

growth_protocol: We used the previously described body-wide Parp14 knockout mice (Cho et al, 2009) in a specific-pathogen-free area at Central Animal Laboratory of the University of Turku with free access to soy-free diet and water ad libitum. Parp14 knockout mice (Cho et al, 2009) were backcrossed for 10 generations to C57BL/6N background before starting experiments. Thereafter, heterozygous mice were inbred to generate homozygous littermates for experiments.

extract_protocol:
Total RNA was isolated from C57BL/6N mice distal colon tissues using TRIsure reagent (BIO-38033, Bioline Gmbh, Germany) and genomic DNA was digested using RNase-free DNase (rDNase) from Machery-Nagel as per the manufacturer’s instructions.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: Salmonella mice experiments were performed according to Barthel and co-workers. The naturally streptomycin-resistant strain S. enterica serovar Typhimurium SL1344 was purchased from the Culture Collection University of Gothenburg (CCUG 51871), Gothenburg, Sweden. Salmonella bacteria were grown for 12h at 37°C in Luria-Bertani with shaking, diluted 1:20 in fresh medium, and sub-cultured for 4h with shaking. Bacteria were washed twice and suspended in ice-cold sterile PBS. Female C57BL/6N mice of age 6-8 weeks were used for Salmonella infection experiments. They were allocated to two treatment groups, i.e., control and Salmonella groups, with similar starting body weight. Water and food were withdrawn 4h before per os (p.o.) treatment with 20 mg of streptomycin (75 μl of sterile solution or 75 μl of sterile water [control]). Afterward, animals were supplied with water and food ad libitum. At 20 h after streptomycin treatment, water and food were withdrawn again for 4 h before the mice were infected with 108 cfu of Salmonella (50 μl suspension in PBS p.o.) or treated with sterile PBS (control). Thereafter, drinking water ad libitum was offered immediately and food 2h post-infection (p.i.). At the indicated times p.i., mice were sacrificed by CO2 asphyxiation, and colon tissue samples were processed for RNA analysis (sample collected in liquid N2).

value: Proximal colon

tag: strain

tag: Sex

value: 10^8 cfu S. Tyhphimurium SL1344


title: Salmonella-infected (S), KO, mice 03

description: Library name: S03KO

tag: tissue


title: Salmonella-infected (S), KO, mice 01

description: Library name: S01KO


title: Salmonella-infected (S), wt, mice 03

description: Library name: S03WT

value: WT


title: baselineLILR077

tag: ethnicity


title: baselineLILR079


title: baselineLILR076


title: baselineLILR073


title: Salmonella-infected (S), wt, mice 02

description: Library name: S02WT


title: Salmonella-infected (S), wt, mice 01

description: Library name: S01WT


title: baselineLILR075


title: PBS-treated (P), KO, mice 02

description: Library name: P02KO

value: PBS


title: C55_ncRNA-seq_1

value: Colorectal Cancer

value: RNA from Whole Cell Lysate


title: B34_ncRNA-seq_4

description:
RNA from whole cell lysate from ΔmiR-100 CC-CR cells
smallRNAseq_human_miR_KO_raw_counts.txt

value: HCA-7 Derived CC-CR {delta}miR-100


title: baselineLILR071

value: Whole blood


title: baselineLILR070


title: PBS-treated (P), KO, mice 01

description: Library name: P01KO


title: baselineLILR083


title: B34_ncRNA-seq_1


title: A375 spontaneously vem-resistant line VRPP3, 3µM vem, replicate 3

city: Iowa City

first: Jesse

last: Riordan

state: IA

address: 375 Newton Road

institute: University of Iowa

description: Library name: VRPP3_3

data_processing:
Transcript pseudoalignment and quantification were performed with kallisto version 0.46.0 using default settings.
Expression levels for each gene were obtained by summing transcript per million (tpm) values across all associated transcripts.
Assembly: Ensembl v94 transcript annotation; GRCh38.p12
Supplementary files format and content: Gene-level expression values in transcripts per million (tpm) in tab-delimited text format

growth_protocol: Parental A375 cells were cultured in DMEM, supplemented with 10% fetal bovine serum, penicillin/streptomycin, and L-glutamate. For 24- and 96-hour BRAFi-treated samples, vemurafenib was added to a final concentration of 3µM for the indicated intervals. All BRAFi-resistant A375 derivative cell lines were continuously cultured in 3µM vemurafenib.

extract_protocol:
To extract total RNA, cells were trypsinized from three independent 10cm plates per condition, rinsed in PBS, and processed using the Direct-zol RNA Miniprep Plus kit (Zymo Research, Irvine, CA). Samples were DNAse-treated.
Sequencing libraries were prepared using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA) and sequenced on a HiSeq-4000 device in 2 x 150bp paired-end format.

value: melanoma

value: 3µM vemurafenib


title: A375 spontaneously vem-resistant line VRPP3, 3µM vem, replicate 1

description: Library name: VRPP3_1


title: baselineLILR082

value: No risk allele

value: Not Hispanic or Latino


title: A375 spontaneously vem-resistant line VRPP3, 3µM vem, replicate 2

description: Library name: VRPP3_2


title: B30_ncRNA-seq_4


title: baselineLILR068

value: Male

value: African American


title: C55_ncRNA-seq_3


title: PBS-treated (P), wt, mice 02

description: Library name: P02WT

value: Female


title: baselineLILR067


title: A375 spontaneously vem-resistant line VRPP2, 3µM vem, replicate 3

description: Library name: VRPP2_3


title: PBS-treated (P), wt, mice 01

description: Library name: P01WT


title: B34_ncRNA-seq_3

value: Colon


title: B30_ncRNA-seq_1


title: A375 spontaneously vem-resistant line VRPP2, 3µM vem, replicate 2

description: Library name: VRPP2_2


title: baselineLILR069

value: LILRB3-4SNPs risk allele


title: A375 spontaneously vem-resistant line VRPP2, 3µM vem, replicate 1

description: Library name: VRPP2_1


title: baselineLILR066


title: baselineLILR065


title: A22_ncRNA-seq_4

description:
RNA from whole cell lysate from ΔmiR-125b CC-CR cells
smallRNAseq_human_miR_KO_raw_counts.txt

value: HCA-7 Derived CC-CR {delta}miR-125b


title: A375 spontaneously vem-resistant line VRPP1, 3µM vem, replicate 3

description: Library name: VRPP1_3


title: A375 spontaneously vem-resistant line VRPP1, 3µM vem, replicate 2

description: Library name: VRPP1_2


title: A22_ncRNA-seq_1


title: baselineLILR063


title: A22_ncRNA-seq_3


title: A375 spontaneously vem-resistant line VRPP1, 3µM vem, replicate 1

description: Library name: VRPP1_1


title: J774A.1 cells, Q11_3

city: zhengzhou city

first: Cunzhen

last: Zhang

state: Henan Province

address: 100 No, kexue road

institute: Zhengzhou university

description:
Library name: Sample9
Q11_3

data_processing:
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.   Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and 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 database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.   Novel transcripts prediction The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.   Quantification of gene expression level Stringtie was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mouse mm10 (GRCm38)
Supplementary files format and content: Column 1 lists the gene identifiers, columns 2-10 contain the transcripts per million (TPM) expression values for each gene in various samples, and column 11 provides the corresponding gene symbols.

extract_protocol:
Cell lysis and homogenization: Collect the cell suspension and add three volumes of TRIzol reagent (for tissue samples, add 1.5 mL TRIzol); Phase separation: Add 1/5 volume of chloroform to the total volume. Cap the tube tightly, vortex for 15 seconds, and incubate at room temperature for 2-3 minutes; Centrifugation: Centrifuge at 2,000 rpm for 10-15 minutes at 4°C; RNA precipitation: Carefully transfer the upper aqueous phase to a new tube and add an equal volume of isopropanol. Invert to mix and incubate at room temperature for 10 minutes; Pelleting RNA: Centrifuge at 12,000 rpm for 10 minutes at room temperature or 4°C; Washing: Carefully remove the supernatant and add 1 mL of 75% ethanol prepared with DEPC-treated water. Wash the tube cap and wall thoroughly and gently flick the tube to resuspend the pellet. For each mL of Total RNA Extraction Reagent used, wash the pellet with 1 mL of 75% ethanol; Final centrifugation: Centrifuge at 12,000 rpm for 3 minutes at room temperature or 4°C. Carefully remove the supernatant, taking care not to lose the RNA pellet; Drying and resuspension: Air-dry the pellet for 2-3 minutes. Resuspend the pellet in 30-100 μL of RNase-free water (DEPC-treated water) and dissolve completely. Measure a small aliquot for quality control, and store the remaining RNA at -80°C
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H - ). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: B30_ncRNA-seq_3


title: A17_ncRNA-seq_4


title: A17_ncRNA-seq_3


title: baselineLILR062


title: J774A.1 cells, Q11_2

description:
Library name: Sample8
Q11_2


title: J774A.1 cells, Q11_1

description:
Library name: Sample7
Q11_1


title: J774A.1 cells, M2_1

description:
Library name: Sample4
M2_1


title: A17_ncRNA-seq_1


title: A375 spontaneously vem-resistant line ECS2.2.2, 3µM vem, replicate 2

description: Library name: ES2.2.2_2


title: baselineLILR061


title: J774A.1 cells, M2_2

description:
Library name: Sample5
M2_2


title: A375 spontaneously vem-resistant line ECS2.2.2, 3µM vem, replicate 3

description: Library name: ES2.2.2_3


title: baselineLILR060


title: J774A.1 cells, Ctrl_3

description:
Library name: Sample3
Ctrl_3


title: A375 spontaneously vem-resistant line ECS2.2.2, 3µM vem, replicate 1

description: Library name: ES2.2.2_1


title: A13_ncRNA-seq_4


title: baselineLILR059


title: J774A.1 cells, M2_3

description:
Library name: Sample6
M2_3


title: A375 spontaneously vem-resistant line ECS2.2.1, 3µM vem, replicate 3

description: Library name: ES2.2.1_3


title: baselineLILR064


title: baselineLILR058


title: A375 spontaneously vem-resistant line ECS2.2.1, 3µM vem, replicate 2

description: Library name: ES2.2.1_2


title: A13_ncRNA-seq_1


title: J774A.1 cells, Ctrl_1

description:
Library name: Sample1
Ctrl_1


title: Macrophages L, oxLDL, 24 hrs

city: Augusta

first: Gabor

last: Csanyi

state: GA

address: 1460 Laney Walker Ave

department: Vascular Biology Center

institute: Augusta University

data_processing:
Basecalling and demultiplexing with Illumina BCLconvert v4.2.4
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Spleen

growth_protocol: Primary splenic monocytes were cultured in RPMI-1640 medium supplemented with 10% FBS, 100 IU/ml of penicillin G and 100 μg/ml streptomycin in humidified incubators at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using an RNA extraction kit (IBI Scientific, Dubuque, Iowa, USA) according to the manufacturer’s protocol. Library preparation was performed with 10 ng of total RNA with a Bioanalyzer RIN score greater than 8.0.
Takara Clontech SMARTer Ultra Low RNA kit

treatment_protocol: Monocytes were differentiated into macrophages using PMA (200 ng/mL, 5 days). Cells were treated with vehicle or ox-LDL (50 µg/mL, 24 hr) prior to RNA extraction.

value: Spleen

value: primary monocyte derived macrophages

tag: treatment (differentiation)

value: PMA (200 ng/mL, 5 days)

tag: agent

value: ox-LDL (50 µg/mL, 24 hr)

value: Wild Type

value: male


title: baselineLILR057

value: Whole blood


title: A12_ncRNA-seq_4

tag: cell line

value: Colorectal Cancer

tag: treatment

value: RNA from Whole Cell Lysate


title: baselineLILR055

tag: genotype


title: baselineLILR056

value: No risk allele


title: A375 spontaneously vem-resistant line EC7.1, 3µM vem, replicate 3

description: Library name: EC7.1_3

tag: cell type

value: melanoma

value: 3µM vemurafenib


title: A12_ncRNA-seq_1


title: baselineLILR053

value: Male

value: Not Hispanic or Latino

value: African American


title: A375 spontaneously vem-resistant line EC7.1, 3µM vem, replicate 2

description: Library name: EC7.1_2


title: A12_ncRNA-seq_3

value: Colon


title: A375 spontaneously vem-resistant line EC7.1, 3µM vem, replicate 1

description: Library name: EC7.1_1


title: Macrophages I, oxLDL, 24 hrs


title: A13_ncRNA-seq_3

value: HCA-7 Derived CC-CR {delta}miR-125b


title: baselineLILR051

value: Female


title: CCCR_4

description:
RNA from whole cell lysate from  CC-CR cells
RNAseq_human_miR_KO_raw_counts.txt

data_processing:
After sequencing, samples (libraries) were demultiplexed and analyzed.  Briefly, reads were trimmed to remove adapter sequences using Cutadapt v2.10)(59) and aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.8a)(61).  Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping.  Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.11.9).  FeatureCounts (v2.0.2)(62) was used to count the number of mapped reads to each gene.  Heatmap3 (63) was used for cluster analysis and visualization.  Significant differential expressed genes with absolute fold change > 2 or < 0.5, and adjusted p value (padj) < 0.05 were determined using DESeq2 (v1.30.1)(64).  Genome Ontology and KEGG pathway over-representation analyses were performed on differentially expressed genes using the WebGestaltR package (NULL)(65).  Gene set enrichment analysis (GSEA) was performed using GSEA package (v4.3.2)(66) on database v2022.1.Hs.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Trizol extraction was completed according to manufacturers protocol.
Bulk RNA sequencing libraries were prepared using Universal RNAseq kits (Tecan), as per manufacturer’s instructions.  Libraries were cleaned (Zymo), checked for quality using the Agilent bioanalyzer, quantified (Qubit), and pooled based on equimolar concentrations of libraries.  Pooled libraries were sequenced using Illumina short-read technology based on PE150 on the NovaSeq6000 (Illumina).

value: HCA-7 Derived CC-CR {delta}miR-100/miR-125b


title: Macrophages H, oxLDL, 24 hrs

value: Spleen

value: primary monocyte derived macrophages

value: PMA (200 ng/mL, 5 days)


title: A375 spontaneously vem-resistant line EC2.1, 3µM vem, replicate 3

description: Library name: EC2.1_3


title: CCCR_3


title: baselineLILR050


title: Macrophages G, oxLDL, 24 hrs

value: ox-LDL (50 µg/mL, 24 hr)

value: Wild Type

value: male


title: A375 spontaneously vem-resistant line EC2.1, 3µM vem, replicate 2

description: Library name: EC2.1_2


title: CCCR_1

value: Colorectal Cancer

value: RNA from Whole Cell Lysate


title: A375 spontaneously vem-resistant line ECS2.2.1, 3µM vem, replicate 1

description: Library name: ES2.2.1_1

value: melanoma


title: baselineLILR049

value: Whole blood

value: No risk allele


title: Macrophages K, oxLDL, 24 hrs


title: A375 spontaneously vem-resistant line EC2.1, 3µM vem, replicate 1

description: Library name: EC2.1_1

value: 3µM vemurafenib


title: Macrophage E, vehicle, 24 hrs

value: vehicle


title: J774A.1 cells, Ctrl_2

description:
Library name: Sample2
Ctrl_2


title: baselineLILR048

value: Not Hispanic or Latino

value: African American


title: A375 spontaneously vem-resistant line EC1.1, 3µM vem, replicate 3

description: Library name: EC1.1_3


title: Macrophage D, vehicle, 24 hrs


title: baselineLILR047

value: Male


title: D84_3

description:
RNA from whole cell lysate from ΔmiR-100/miR-125b CC-CR cells
RNAseq_human_miR_KO_raw_counts.txt

value: Colon

value: HCA-7 Derived CC-CR {delta}miR-100/miR-125b


title: Macrophage C, vehicle, 24 hrs

value: Spleen

value: primary monocyte derived macrophages


title: D82_4


title: D84_1


title: A375 spontaneously vem-resistant line EC1.1, 3µM vem, replicate 1

description: Library name: EC1.1_1


title: A375 spontaneously vem-resistant line EC1.1, 3µM vem, replicate 2

description: Library name: EC1.1_2


title: baselineLILR045


title: Macrophage A, vehicle, 24 hrs

value: PMA (200 ng/mL, 5 days)


title: baselineLILR043

value: LILRB3-4SNPs risk allele

value: Female


title: Macrophages J, oxLDL, 24 hrs

value: ox-LDL (50 µg/mL, 24 hr)

value: Wild Type

value: male


title: A375 parental cells, 3µM vem-treated 96h, replicate 3

description: Library name: A375-96hvem_3

value: melanoma


title: A375 parental cells, 3µM vem-treated 96h, replicate 2

description: Library name: A375-96hvem_2


title: baselineLILR046

value: Whole blood

value: No risk allele


title: D82_1

value: Colorectal Cancer

value: RNA from Whole Cell Lysate


title: Macrophage B, vehicle, 24 hrs

value: vehicle


title: D84_4


title: baselineLILR042

value: Not Hispanic or Latino

value: African American


title: Monocytes 8, oxLDL, 24 hrs

value: primary monocyte


title: Monocytes 9, oxLDL, 24 hrs

value: Spleen


title: baselineLILR041


title: Monocytes 7, oxLDL, 24 hrs


title: A375 parental cells, 3µM vem-treated 96h, replicate 1

description: Library name: A375-96hvem_1

value: 3µM vemurafenib


title: C55_3

value: Colon

value: HCA-7 Derived CC-CR {delta}miR-100/miR-125b


title: A375 parental cells, 3µM vem-treated 24h, replicate 3

description: Library name: A375-24hvem_3


title: baselineLILR040

value: Male


title: A375 parental cells, 3µM vem-treated 24h, replicate 2

description: Library name: A375-24hvem_2


title: Monocytes 6, vehicle, 24 hrs


title: baselineLILR038

value: LILRB3-4SNPs risk allele

value: Female


title: B34_4

description:
RNA from whole cell lysate from ΔmiR-100 CC-CR cells
RNAseq_human_miR_KO_raw_counts.txt

value: HCA-7 Derived CC-CR {delta}miR-100


title: baselineLILR037


title: A375 parental cells, 3µM vem-treated 24h, replicate 1

description: Library name: A375-24hvem_1

value: melanoma


title: C55_1


title: A375 parental cells, vehicle-treated, replicate 3

description: Library name: A375_3

value: vehicle (DMSO)


title: B34_3


title: Monocytes 4, vehicle, 24 hrs

value: Wild Type

value: male


title: baselineLILR036

value: Whole blood

value: No risk allele


title: A375 parental cells, vehicle-treated, replicate 2

description: Library name: A375_2


title: Monocytes 3, vehicle, 24 hrs

value: vehicle


title: baselineLILR035

value: Not Hispanic or Latino

value: African American


title: B34_1

value: Colorectal Cancer

value: RNA from Whole Cell Lysate


title: baselineLILR033


title: A375 parental cells, vehicle-treated, replicate 1

description: Library name: A375_1


title: C55_4

value: Colon


title: Monocytes 2, vehicle, 24 hrs

value: Spleen

value: primary monocyte


title: pooled cell lines, Multi-Seq

description: multi-seq library with barcode x treatment assignments

data_processing:
Raw single-cell FASTQ files were used as input into the 10X Cell Ranger pipeline with default parameters. Briefly, reads were aligned to the hg38 transcriptome using STAR generating a filtered feature-barcode matrix and bam alignment file.
Pooled scRNA-Seq experiments were demultiplexed into individual cell lines using Demuxlet with the CB tag, setting the fixed mixing proportion, alpha, to 0.5. Demultiplexing of single cell barcodes into drug treatments using hashtag oligos (HTOs) was performed using pymulti from the scEasyMode python library (https://github.com/johnnyUCSF/scEasyMode) , Multiplexed scRNA-Seq count matrices were processed using scanpy. Counts were normalized (normalize_per_cell) and, log-transformed (log1p). Additionally, droplets predicted as doublets by demuxlet were removed. Normalized count matrices were used to calculate PCA, leiden clusters, and UMAP representations.
Assembly: hg38 cellranger reference
Supplementary files format and content: cellranger counts outputs: barcodes.tsv.gz features.tsv.gz matrix.mtx.gz
Supplementary files format and content: processed anndata objects with cell line and drug treatment calls
Library strategy: Multi-seq

source_name: pooled cell lines

value: Mixed Sample (Melanoma, Melanoma, Melanoma, Pancreatic Cancer, Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC)) Non-Small Cell Lung Cancer (NSCLC), Non-Small Cell Lung Cancer (NSCLC), Melanoma, Melanoma

value: Mixed Sample (A375, HTT114, SKMEL2, MiaPaca-2, H358, A549, H1299, H1975, H23, MeWo, SKMEL28)

value: mixed sample (DMSO, ARS-1620, Vemurafenib)


title: Monocytes 1, vehicle, 24 hrs


title: B30_3

value: HCA-7 Derived CC-CR {delta}miR-100


title: Monocytes 11, oxLDL, 24 hrs

value: ox-LDL (50 µg/mL, 24 hr)


title: B30_4


title: Monocytes 5, vehicle, 24 hrs

value: Wild Type


title: pooled cell lines, GEX

description: pooled 10x gene expresison from cell lines, cellranger outputs, demuxlet output and processed anndata included

data_processing:
Raw single-cell FASTQ files were used as input into the 10X Cell Ranger pipeline with default parameters. Briefly, reads were aligned to the hg38 transcriptome using STAR generating a filtered feature-barcode matrix and bam alignment file.
Pooled scRNA-Seq experiments were demultiplexed into individual cell lines using Demuxlet with the CB tag, setting the fixed mixing proportion, alpha, to 0.5. Demultiplexing of single cell barcodes into drug treatments using hashtag oligos (HTOs) was performed using pymulti from the scEasyMode python library (https://github.com/johnnyUCSF/scEasyMode) , Multiplexed scRNA-Seq count matrices were processed using scanpy. Counts were normalized (normalize_per_cell) and, log-transformed (log1p). Additionally, droplets predicted as doublets by demuxlet were removed. Normalized count matrices were used to calculate PCA, leiden clusters, and UMAP representations.
Assembly: hg38 cellranger reference
Supplementary files format and content: cellranger counts outputs: barcodes.tsv.gz features.tsv.gz matrix.mtx.gz
Supplementary files format and content: processed anndata objects with cell line and drug treatment calls


title: B30_1


title: baselineLILR031

value: Male


title: Monocytes 10, oxLDL, 24 hrs

value: male


title: SCC13 cells, CELF2-KD 2

city: Austin

first: Liu

last: Liang

address: 801 16th Ave NE

institute: The HorMel Institute

data_processing:
Sequencing reads were mapped to the human reference genome (NCBI/build37.2) using Hisat2.
Genes differentially expressed between CELF2-KD and control cells were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: Homo_sapiens.GRCh38.97
Supplementary files format and content: RawCountsLiu5_008.txt

growth_protocol: Human SCC13 cells were cultured in CnT-07 medium supplement and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated from cultured human SCC cells by using the RNeasy kit
Illumina TruSeq libraryprep kit

treatment_protocol: SCC13 cells were infected with lentivirus that expressed either scrambled shRNA (shScr) or CELF2-targeting shRNA (shCELF2)..

value: skin cancer cell line

value: WT

value: CELF2-targeting shRNA


title: baselineLILR029

value: Whole blood

value: No risk allele

value: Not Hispanic or Latino

value: African American


title: SCC13 cells, CELF2-KD 1


title: A22_3

description:
RNA from whole cell lysate from ΔmiR-125b CC-CR cells
RNAseq_human_miR_KO_raw_counts.txt

value: Colon

value: HCA-7 Derived CC-CR {delta}miR-125b

value: Colorectal Cancer

value: RNA from Whole Cell Lysate


title: baselineLILR028

value: Female


title: baselineLILR024


title: A22_4


title: A17_4


title: baselineLILR023


title: A17_3


title: baselineLILR032


title: lung metastasis tumor 34

city: Beijing

first: Xiaohong

address: 1,DongJiaoMinXiang Street, DongCheng District,Beijing, P.R.China.100730

department: Department of Otolaryngology Head and Neck Surgery

institute: Beijing Tongren Hospital, Capital Medical University

description:
Library name: LC9
LC9

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Ecxel file includes TPM values for each Sample.

source_name: tumor

extract_protocol:
Appropriate tissue samples were collected into corresponding numbered grinding tubes, and 1.5 mL of TRIzol lysis reagent was added. Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction. The concentration, RNA integrity number, 28S/18S ratio, and fragment size of total RNA were determined using the Agilent 2100 Bioanalyzer.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). Samples meeting quality standards were used for library construction and sequencing on an MGISEQ-2000RS platform.

value: tumor


title: BMM, Irgm_IFNAR-KO_2

city: Durham

first: Gregory

middle: Alan

last: Taylor

state: NC

address: DUMC Box 3003

department: Medicine

institute: Duke University

description:
SP 100 cycles
8199-S11

data_processing:
Read QC, adapter removal and trimming was done via fastp
Alignments and gene-counts were obtained via STAR
Differential expression was conducted within the DESeq2 fraimwork
Assembly: Reads were mapped to assembly GRCm39
Assembly: Gene model was downloaded from Ensembl version 110
Supplementary files format and content: Tables of counts read counts provided by STAR

growth_protocol: Irgm1-/- (Collazo CM, 2001) and IFNAR/Irgm1-/- (Rai P, 2021; Rai P, 2023) were backcrossed to C57BL/6 mice (wild-type). All mice were housed and maintained under procedures approved by the Institutional Animal Care and Use Committees at the Duke University and Durham VA Medical Centers. Primary murine bone marrow-derived macrophages (BMM) were isolated from the tibia and femurs of 2- to 4-month-old male and female mice and cultured according to standard procedures described previously (Henry S, 2007). The bone marrow was flushed from the bones using a 27G needle fitted to a syringe filled with DMEM (Life Technologies); the marrow was dispersed by drawing through the needle three to four times; and red cells were lysed with ACK lysing buffer (Life Technologies). Adherent cells were cultured for 6 days in BMM medium [DMEM supplemented with 10% (v/v) FBS (Hyclone) and 20% (v/v) L929 cell-conditioned medium]. The cells were cultured on Petri dishes that were not cell culture-treated, resulting in cultures that were loosely adherent and easily removed from the plates with cell dissociation buffer (13150-016, Gibco/Thermo Fisher). 24 h prior to all experiments, the cells were placed in medium lacking L929-conditioned media [DMEM (11995, Gibco/ThermoFisher), supplemented with 10% (v/v) FBS and 100 units/ml penicillin/100 µg/ml streptomycin (15140, GIBCO/ThermoFisher)] on coverslips or cell culture plates. All primary cells and cell lines were grown and maintained in a humidified atmosphere of 5% CO2 at 37°C. Where appropriate, the following were added to the growth media as indicated in the text: 100 U/mL interferon (IFN)-γ(IF005, EMD Millipore), IFNAR neutralizing antibodies, 50 µM fenofibrate (F6020, Sigma), 1 µM Torin-1 (inh-tor1, InvivoGen), 0.1 µM bafilomycin A1 (SC201550, Santa Cruz Biotechnology), and/or 10 µM C75 (C5490, Sigma).

extract_protocol:
Total RNA was extracted from cell pellets using the RNeasy Plus Mini Kit from Qiagen (ID: 74134). mRNA was enriched from total RNA and reversed transcribed into cDNA.
Sequencing libraries were built using the Kapa mRNA HyperPrep Kit from Roche (Code: KK8581) and libraries were pooled to equimolar concentration.

value: BMM


title: BMM, Irgm1-KO_4

description:
SP 100 cycles
8199-S6

source_name: Primary murine bone marrow-derived macrophages


title: BMM, Irgm_IFNAR-KO_1

description:
SP 100 cycles
8199-S10

value: Primary murine bone marrow-derived macrophages


title: BMM, Irgm_IFNAR-KO_3

description:
SP 100 cycles
8199-S12


title: baselineLILR022

value: Male


title: baselineLILR021


title: A17_1


title: lung metastasis tumor 32

description:
Library name: LC7
LC7


title: A13_4


title: BMM, Irgm1-KO_3

description:
SP 100 cycles
8199-S5


title: BMM, Irgm_IFNAR-KO_4

description:
SP 100 cycles
8199-S9


title: SCC13 cells, shRNA control 2

value: scrambled shRNA (shScr)


title: lung metastasis tumor 31

description:
Library name: LC6
LC6


title: baselineLILR019


title: A22_1


title: BMM, Irgm1-KO_2

description:
SP 100 cycles
8199-S3


title: lung metastasis tumor 33

description:
Library name: mLC8
mLC8


title: BMM, Irgm1-KO_1

description:
SP 100 cycles
8199-S2


title: A13_3


title: SCC13 cells, shRNA control 1

value: skin cancer cell line


title: lung metastasis tumor 30

description:
Library name: LC5
LC5


title: A13_1


title: baselineLILR017


title: lung metastasis tumor 29

description:
Library name: LC40
LC40


title: BMM, WT_4

description:
SP 100 cycles
8199-S8

value: WT


title: baselineLILR016


title: lung metastasis tumor 28

description:
Library name: LC4
LC4


title: BMM, WT_3

description:
SP 100 cycles
8199-S7


title: A12_4


title: BMM, WT_2

description:
SP 100 cycles
8199-S4


title: lung metastasis tumor 27

description:
Library name: mLC3
mLC3


title: A12_3


title: baselineLILR015

value: LILRB3-4SNPs risk allele


title: baselineLILR020

value: Whole blood


title: baselineLILR014


title: BMM, WT_1

description:
SP 100 cycles
8199-S1


title: A12_1


title: baselineLILR013


title: CC_Ago2_RIP_ncRNA-seq3

description:
RNA seq from RNA collected from AGO2 RNA immunoprecipitation from CC cells
smallRNAseq_human_AGO2_IP_raw_counts.txt

growth_protocol: CC and CC-CR CRC cells were obtained from the Coffey lab (Lu et al., 2017).  All cell lines were confirmed to be free of mycoplasma contamination (VenorTMGeM Mycoplasma Detection Kit, PCR-based, Sigma Aldrich Cat #MP0025).  Cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Corning) supplemented with 10% fetal bovine serum (FBS, Corning), 1% L-glutamine (200 nM, Gibco), 1% MEM nonessential amino acids (Sigma Aldrich), and 1% penicillin-streptomycin (10,000 U/mL, Gibco) in 5% CO2 at 37°C.  Cells were passaged a maximum of 8 times before discarding

treatment_protocol: For immunoprecipitation, anti-AGO2 (clone 11A9 antibody; MABE253, Sigma-Aldrich) or control IgG antibodies were used.  Ten 150cm dishes of either CC or CC-CR cells were grown to 95% confluency.  Cells were then scraped in ice cold PBS and centrifuged to collect cell pellets in ice cold lysis buffer (20mM Tris HCl pH 7.5, 150 mM KCl, 0.5% NP40, 2mM EDTA, 1mM NaF, 0.5mM DTT).  After centrifugation of insoluble cell debris, cell lysates were incubated with Dynabeads.  Prior to cell lysis, Dynabeads™ Protein G (ThermoFisher, 10003D) were conjugated with antibodies by incubating overnight with rotation at 4°C and washed two times with ice cold lysis buffer.  Cell lysates were then added to the conjugated beads and incubated at 4°C for six hours.  Beads were gently washed with fresh lysis buffer and proteins were eluted.  For RNA isolation, beads were incubated with DNase and Proteinase K for 10 minutes at room temperature.  Trizol was then added and incubated at room temp for 10 minutes and RNA was isolated.

value: HCA-7 Derived CC

value: AGO2 RNA Immunoprecipitation


title: lung metastasis tumor 25

description:
Library name: LC35
LC35


title: OVE26 Lrg1-/- 3

data_processing:
The raw fastq sequences were aligned to mm10 genome with 10x cellRanger.
Gene and cell QC was performed with Seurat by removing the genes expressing in less than 3 cells and cells expressing less than 200 genes.
Assembly: mm10
Supplementary files format and content: Sparse matrix of the raw counts of gene-cell expression.
Supplementary files format and content: Cellranger processed filtered matrix for each sample, including barcodes.tsv, feature.tsv and matrix.mtx.

source_name: Whole kidney

extract_protocol:
To optimize the representation of all kidney cells, glomeruli were first isolated from harvested mouse kidneys using magnetic beads (16), and kidney cells from glomerular and non-glomerular fractions were prepared separately and pooled together per mouse kidney prior to downstream processing. The glomerular fraction was prepared as described previously, and the non-glomerular fraction was prepared with the following modifications: harvested fraction was incubated in the digestion buffer for 10 min at 37°C, and dissociated cells were filtered through 40-micron cell strainers.
Kidney single-cells were processed using the Chromium Single Cell 3’ kit (v3) of 10x Genomics according to the manufacturer’s protocol.
The final constructed single-cell libraries were sequenced by Illumina Novaseq machine with total reads per cell targeted for a minimum of 30,000.

value: Whole kidney

value: OVE26 Lrg1-/-


title: CC_Ago2_RIP_ncRNA-seq2

value: Colon


title: lung metastasis tumor 23

description:
Library name: LC32
LC32


title: baselineLILR012

value: No risk allele

value: Not Hispanic or Latino

value: African American


title: OVE26 Lrg1-/- 2


title: CC_Ago2_RIP_ncRNA-seq1

value: Colorectal Cancer


title: baselineLILR011


title: baselineLILR010


title: CCCR_Ago2_RIP_ncRNA-seq3

description:
RNA seq from RNA collected from AGO2 RNA immunoprecipitation from CC-CR cells
smallRNAseq_human_AGO2_IP_raw_counts.txt

value: HCA-7 Derived CC-CR


title: OVE26 Lrg1-/- 1


title: CCCR_Ago2_RIP_ncRNA-seq1


title: baselineLILR009


title: OVE26 2


title: OVE26 1


title: lung metastasis tumor 26

description:
Library name: LC37
LC37

value: tumor


title: lung metastasis tumor 19

description:
Library name: LC26
LC26


title: lung metastasis tumor 22

description:
Library name: LC31
LC31


title: lung metastasis tumor 21

description:
Library name: LC3
LC3


title: CC_WC_ncRNA-seq3

description:
RNA seq from RNA collected from Whole Cell Lysates from CC cells
smallRNAseq_human_AGO2_IP_raw_counts.txt

value: Whole Cell Lysate


title: baselineLILR006

value: Female


title: lung metastasis tumor 18

description:
Library name: LC25
LC25


title: Wild type 2


title: baselineLILR008

value: Male


title: Wild type 4

value: WT


title: CC_WC_ncRNA-seq2


title: lung metastasis tumor 17

description:
Library name: LC24
LC24


title: baselineLILR005


title: lung metastasis tumor 20

description:
Library name: LC28
LC28


title: baselineLILR007


title: CC_WC_ncRNA-seq1


title: Wild type 1


title: CCCR_WC_ncRNA-seq3

description:
RNA seq from RNA collected from Whole Cell Lysates from CC-CR cells
smallRNAseq_human_AGO2_IP_raw_counts.txt


title: lung metastasis tumor 24

description:
Library name: LC34
LC34


title: baselineLILR003


title: CCCR_WC_ncRNA-seq2


title: lung metastasis tumor 16

description:
Library name: LC23
LC23


title: baselineLILR004

value: LILRB3-4SNPs risk allele


title: CCCR_WC_ncRNA-seq1


title: Wild type 3


title: baselineLILR001

value: Whole blood


title: WT

city: Tianjin

first: Zhen

last: Yang

address: Weijin Street

institute: Nankai University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastqformat were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC  the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were Hisat2 (v2.0.5)aligned to the reference genome using
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: xlsx files includes raw counts for each Sample

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained。


title: CC_Ago2_RIP_3

description:
RNA seq from RNA collected from AGO2 RNA immunoprecipitation from CC cells
RNAseq_human_AGO2_IP_raw_counts.txt

value: HCA-7 Derived CC


title: sgRNA_day10

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: breast tumor

extract_protocol:
Mice were euthanized and dissected at different days after tumor implantation to collect tumor tissues. Tumor tissues were cut into pieces and enzymatically digested with 1 mg/mL collagenase I, 1 mg/mL collagenase IV, and 300 μg/mL DNase I at 37 °C for 45 min. The suspension was then filtered through a 70 μm Nylon Cell Strainer (Corning Life Sciences) and centrifuged at 500 g for 5 min. Erythrocytes were removed by hypotonic lysis for 5 min at room temperature.  The single cells were then incubated for 30 min with FcR blocking anti-mouse CD16/32 antibody followed by incubation with PE anti-mouse CD45 antibody for another 30 min on ice. The CD45+ immune cells were sorted by SONY MA900 Multi-Application Cell Sorter.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, sorted immune 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: breast tumor

value: immune cells

value: sgRNA

tag: time

value: day 10


title: lung metastasis tumor 14

description:
Library name: LC21
LC21


title: CC_Ago2_RIP_1

value: Colon

value: AGO2 RNA Immunoprecipitation


title: sgNC_day10

value: control


title: lung metastasis tumor 13

description:
Library name: LC20
LC20


title: lung metastasis tumor 12

description:
Library name: LC2
LC2


title: CCCR_Ago2_RIP_3

description:
RNA seq from RNA collected from AGO2 RNA immunoprecipitation from CC-CR cells
RNAseq_human_AGO2_IP_raw_counts.txt

value: Colorectal Cancer


title: CCCR_Ago2_RIP_2

value: HCA-7 Derived CC-CR


title: K562_FB23-2_1

city: Rome

first: Alessandro

last: Fatica

address: P.ale Aldo Moro 5

department: Biology and Biotechnologies

country: Italy

institute: Sapienza Un iversity of Rome

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C

data_processing:
Data was extracted using Agilent Feature Extraction software. The probe signals passing "P" or "M" QC flags in at least 1 sample were retained for further analysis.
IP (Cy5-labelled) intensities were normalized as relative intensities by the RNA spike-in calibration controls. The “m6A quantity” was calculated for the m6A methylation amount of each transcript based on the IP (Cy5-labelled) normalized intensities.The m6A quantity is based on the normalized intensities of IP signals (raw signals of Cy5-labelled IP RNA are normalized with the average log2-scaled Spike-in RNA intensities). Meanwhile, the percentage of m6A methylation (%Modified) for a transcript was calculated based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities.

label_protocol: "IP" and "Sup" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Chronic myeloid leukemia cell lines K562 was cultured in RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum, 1× penicillin-streptomycin at 37°C under an atmosphere containing 5% CO2.

extract_protocol: Total RNAs were purified with  Directzol RNA Miniprep kit (Zymo) and were immunoprecipitated with anti-N6-methyladenosine(m6A) antibody. The immunoprecipitated "IP" fraction contained enriched m6A methylated RNAs, and the supernatant " Sup" fraction contained unmodified RNAs

treatment_protocol: Cells were treated for 48 hours with 5 mM FB23-2 or DMSO

value: CML cell line

source_name: supernatant


title: KO


title: sgRNA_day8

value: day 8


title: sgNC_day8


title: K562_FB23-2_2


title: lung metastasis tumor 10

description:
Library name: LC18
LC18

value: tumor


title: K562_DMSO_3

source_name: K562 DMSO


title: K562_DMSO_2


title: lung metastasis tumor 11

description:
Library name: LC19
LC19


title: CCCR_Ago2_RIP_1


title: sgNC_day6

value: day 6


title: K562_DMSO_1


title: sgRNA_day6


title: K562_FB23-2_3


title: lung metastasis tumor 8

description:
Library name: mLC16
mLC16


title: lung metastasis tumor 15

description:
Library name: LC22
LC22


title: CC_WC_3

description:
RNA seq from RNA collected from Whole Cell Lysates from CC cells
RNAseq_human_AGO2_IP_raw_counts.txt

value: Whole Cell Lysate


title: WT

city: Munich

first: Jan

middle: M

last: Deussing

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

data_processing:
10x Genomics CellRanger v. 3.0.2
Filtered count matrices obtained from CellRanger were imported in Seurat v 3.1.3 for quality control and clustering.
Cells with less than 320 genes, and mitochondrial gene content higher than 25%, and putative droplets identified with the package scran v.1.14.6 were removed before clustering.
Clustering was performed on lognormalized and scaled expression data using the top 4000 variable genes. 25 PCs and a resolution of 1.2 were used for the final clustering.
Assembly: mm10
Supplementary files format and content: filtered count matrices generated by CellRanger
Supplementary files format and content: CSV table containing metadata for each cell

source_name: ventral hippocampus (vHPC)

extract_protocol:
WT and mutant nimals were sacrificed and perfused in cold PBS. The vHPC was dissected from the fresh brain, and digested in Papain supplemented with DNAse I. After dissociation and filtering, cells were concentrated to 1,000,000 cells/ml and loaded on a v3 chip in the 10x Genomics Chromium Controller.
Libraries were prepared using the the 10x Genomics NEXT-GEM Single Cell 3’ Reagent Kits according to the manufacturer’s protocol.
3' mRNA-seq

value: ventral hippocampus (vHPC)

value: brain

value: ADCY2-V151 (wt)

tag: age

value: 11-12 weeks old

value: male

value: C57BL/6J x C57BL/6N


title: CC_WC_2

value: HCA-7 Derived CC


title: MT


title: CC_WC_1

value: Colon


title: D82_3

value: HCA-7 Derived CC-CR {delta}miR-100/miR-125b

value: RNA from Whole Cell Lysate


title: CCCR_WC_2

description:
RNA seq from RNA collected from Whole Cell Lysates from CC-CR cells
RNAseq_human_AGO2_IP_raw_counts.txt

value: Colorectal Cancer


title: CCCR_WC_1

value: HCA-7 Derived CC-CR


title: head control AGO2, P3

city: Gif-sur-Yvette

first: Katarzyna

last: Siudeja

address: 1, Avenue de la Terrasse

country: France

institute: Institute for Integrative Biology of the Cell (I2BC), INSERM U1280, CEA, CNRS, Université Paris-Saclay

description: Library name: D1255T94

data_processing:
Illumina RNA-seq libraries were aligned to the masked reference genome plus chrTE, which contained consensus transposable element sequences for D. melanogaster, using STAR 2.7.10a with the following parameters: --sjdbOverhang 100 --outFilterMultimapNmax 1 --winAnchorMultimapNmax 10 --outMultimapperOrder Random --outFilterMismatchNoverLmax 0.3 --quantMode GeneCounts quantification mode. The expression count tables were grouped for all samples, and the counts were normalized using TMM normalization method from the edgeR R package.
Raw ONT cDNA reads were basecalled with guppy v6.0.1 using the following parameters for the flowcell and sequencing kit: --flowcell FLO-MIN106 --kit SQK-DCS109. Basecalled reads were trimmed and oriented with pychopper v2, developed by ONT. Basecalled reads were aligned to the masked reference genome plus chrTE, which contained consensus transposable element sequences for D. melanogaster, using minimap2 with the -x splice preset and the --secondary=no parameter. Read counts were quantified using featureCounts v2.0.1 from the Subread package with the following parameters: -Q 5 -L.
Assembly: dm6.48 and consensus transposable element sequences for D. melanogaster
Supplementary files format and content: tabulated text files with raw and normalized counts

organism: Drosophila melanogaster

source_name: head

growth_protocol: Flies were maintained on a standard medium at 25°C with a day/night light cycle. Adult progeny was collected over 2–4 days after eclosion and kept at a density of 25-30 flies/tube (mixed sexes). Flies were flipped to fresh tubes every 2-3 days until needed. For aging experiments 3 time-points were analyzed: young 5-7-day-old, mid-age 20-25-days-old and aged 50-60-days-old.

extract_protocol:
Gut and head tissues were dissected in cold, RNase‐free PBS, transferred to 100 μl of TRIzol Reagent (Thermo Fisher Scientific), homogenized with a plastic pestle and snap‐frozen in liquid nitrogen for storage at −80°C. Upon thawing, samples were further processed according to the TRIzol Reagent manufacturer’s protocol. Purified RNA was treated with DNase (Ambion) for 1 h at 37°C, further purified with phenol‐chloroform extraction and isopropanol precipitation, and resuspended in RNase‐free water. All samples had A260/280 ratios above 1.9 and A260/230 ratios above 2.0. RNA integrity was checked on Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano Kit and concentrations were assayed with the Qubit RNA Broad Range Assay Kit (Thermo Fisher Scientific).
For the short-read transcriptome analysis, 700ng of total RNA was used to prepare libraries according to the TruSeq Stranded mRNA protocol (Illumina). Samples were processed in biological triplicates. 2X100 bp paired‐end sequencing was performed on Novaseq (Illumina). For long-read Oxford Nanopore (ONT) cDNA sequencing, we first prepared mRNA with Dynabeads mRNA Purification Kit (Invitrogen #61006) starting from 100 mg of DN-ase digested total RNA, according to the manufacturer’s protocol. mRNA concentration was quantified with the Qubit RNA Broad Range Assay Kit (Thermo Fisher Scientific) and sample quality was checked on Bioanalyzer (Agilent). Samples were then prepared according to the protocol for ONT Direct cDNA sequencing (SQK-DCS109, Oxford Nanopre), using 150 ng of purified mRNA as input. Samples were run on MinION using R9.4.1 flow cells (Oxford Nanopore Technologies) and 48 h‐long sequencing runs.

value: head

value: whole tissue

value: w1118; rover2R:14M/rover2R:14M;

value: no treatment

tag: batch

value: mixed ages


title: lung metastasis tumor 7

description:
Library name: LC16
LC16

value: tumor


title: BMM, Irgm1KO_fenofibrate_2

description:
1.5B 50 cycles
10098-S10_Irgm1KO_fenofibrate

value: Primary murine bone marrow-derived macrophages

value: BMM

value: fenofibrate


title: CCCR_WC_3

value: Whole Cell Lysate


title: lung metastasis tumor 3

description:
Library name: LC11
LC11


title: head control AGO2, P2

description: Library name: D1255T93


title: head AGO2, P3

description: Library name: D1255T88


title: head control AGO2, P1

description: Library name: D1255T92


title: BMM, Irgm1KO_fenofibrate_4

description:
1.5B 50 cycles
10098-S12_Irgm1KO_fenofibrate


title: BMM, Irgm1KO_control_3

description:
1.5B 50 cycles
10098-S3_Irgm1KO_control

value: control


title: BMM, Irgm1KO_fenofibrate_3

description:
1.5B 50 cycles
10098-S11_Irgm1KO_fenofibrate


title: head AGO2, P2

description: Library name: D1255T87


title: lung metastasis tumor 5

description:
Library name: LC13
LC13


title: lung metastasis tumor 4

description:
Library name: LC12
LC12


title: lung metastasis tumor 9

description:
Library name: LC17
LC17


title: gut control AGO2, P2

description: Library name: D1255T90

source_name: gut

value: gut


title: gut control AGO2, P3

description: Library name: D1255T91


title: head AGO2, P1

description: Library name: D1255T86


title: U2OS cells, ZBTB48 KO IFNg, RNA-seq rep4

city: Singapore

first: Dennis

last: Kappei

address: 14 Medical Drive, #11-01 (Bench 11), Centre for Translational Medicine

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

data_processing:
Reads aligned to human reference genome GRCh38 using STAR v2.7.9a, allowing upto 4 mismatches per pair
Filtered for unique reads using NH:i field
Quantified using featureCounts v2.4.0
DESeq2 (v1.40.1) for differential expression, normal shrinkage estimation applied
bigwig tracks generated using bamCoverage (deeptools v3.5.1) with cpm normalization
Assembly: GRCh38 (GCA_000001405.15)
Supplementary files format and content: tab-delimited text file containing raw counts for all samlpes
Supplementary files format and content: bigwig track for each sample, signal

growth_protocol: U2OS cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 4.5 g/l glucose, 4 mM glutamine, 1 mM sodium pyruvate and supplemented with 10% foetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with additional on‐column DNaseI digestion following the manufacturer's instructions.
RNA-seq (stranded mRNA) library prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: For induction of CIITA, 250U/ml IFNg was added to the culture medium and cells were incubated for 24 hours.

value: ZBTB48 Knockout

value: IFNg

tag: clone


title: BMM, Irgm1KO_fenofibrate_1

description:
1.5B 50 cycles
10098-S9_Irgm1KO_fenofibrate


title: lung metastasis tumor 2

description:
Library name: LC10
LC10


title: BMM, WT_fenofibrate_3

description:
1.5B 50 cycles
10098-S15_WT_fenofibrate

value: WT


title: lung metastasis tumor 1

description:
Library name: LC1
LC1


title: BMM, Irgm1KO_control_2

description:
1.5B 50 cycles
10098-S2_Irgm1KO_control


title: BMM, WT_fenofibrate_2

description:
1.5B 50 cycles
10098-S14_WT_fenofibrate


title: U2OS cells, ZBTB48 KO IFNg, RNA-seq rep1


title: lung metastasis tumor 6

description:
Library name: LC14
LC14


title: U2OS cells, ZBTB48 KO IFNg, RNA-seq rep5


title: lung normal tissue 14

description:
Library name: mLAP3
mLAP3

source_name: normal tissue

value: normal tissue


title: BMM, Irgm1KO_control_1

description:
1.5B 50 cycles
10098-S1_Irgm1KO_control


title: BMM, WT_fenofibrate_1

description:
1.5B 50 cycles
10098-S13_WT_fenofibrate


title: U2OS cells, WT IFNg, RNA-seq rep5


title: gut AGO2, P3

description: Library name: D1255T85


title: guts old w1118, P2

description: Library name: D037T111

value: old flies (50-60 days)


title: lung normal tissue 17

description:
Library name: LAP6
LAP6


title: BMM, WT_fenofibrate_4

description:
1.5B 50 cycles
10098-S16_WT_fenofibrate


title: gut control AGO2, P1

description: Library name: D1255T89


title: U2OS cells, ZBTB48 KO IFNg, RNA-seq rep3


title: lung normal tissue 16

description:
Library name: LAP5
LAP5


title: gut AGO2, P1

description: Library name: D1255T83


title: lung normal tissue 12

description:
Library name: LAP3
LAP3


title: BMM, Irgm1KO_control_4

description:
1.5B 50 cycles
10098-S4_Irgm1KO_control


title: lung normal tissue 15

description:
Library name: LAP4
LAP4


title: lung normal tissue 11

description:
Library name: LAP28
LAP28


title: gut AGO2, P2

description: Library name: D1255T84


title: lung normal tissue 18

description:
Library name: mLAP8
mLAP8


title: U2OS cells, WT IFNg, RNA-seq rep2


title: BMM, WT_control_4

description:
1.5B 50 cycles
10098-S8_WT_control


title: U2OS cells, WT IFNg, RNA-seq rep4


title: lung normal tissue 13

description:
Library name: LAP32
LAP32


title: guts old w1118, P1

description: Library name: D037T110


title: U2OS cells, ZBTB48 KO, RNA-seq rep5


title: Heads old, P3

description: Library name: D091T12

value: head

value: w1118; rover2R:14M /UAS-2xGFP/+ ; ProsGAL4/+


title: guts old w1118, P3

description: Library name: D037T112

value: whole tissue


title: U2OS cells, WT IFNg, RNA-seq rep3


title: BMM, WT_control_3

description:
1.5B 50 cycles
10098-S7_WT_control


title: BMM, WT_control_2

description:
1.5B 50 cycles
10098-S6_WT_control


title: BMM, WT_control_1

description:
1.5B 50 cycles
10098-S5_WT_control


title: guts young w1118, P3

description: Library name: D037T109

value: no treatment

value: young flies (5-7 days)


title: guts young w1118, P1

description: Library name: D037T107


title: guts young w1118, P2

description: Library name: D037T108


title: lung normal tissue 9

description:
Library name: LAP25
LAP25


title: lung normal tissue 7

description:
Library name: mLAP16
mLAP16


title: Heads old, P1

description: Library name: D091T10


title: U2OS cells, WT IFNg, RNA-seq rep1


title: lung normal tissue 6

description:
Library name: LAP14
LAP14


title: U2OS cells, ZBTB48 KO, RNA-seq rep2


title: lung normal tissue 8

description:
Library name: LAP2
LAP2


title: lung normal tissue 10

description:
Library name: LAP26
LAP26


title: Heads old, P2

description: Library name: D091T11


title: U2OS cells, ZBTB48 KO, RNA-seq rep3


title: Heads young, P3

description: Library name: D091T06


title: U2OS cells, ZBTB48 KO, RNA-seq rep4


title: lung normal tissue 5

description:
Library name: LAP13
LAP13


title: U2OS cells, WT, RNA-seq rep5


title: lung normal tissue 4

description:
Library name: LAP12
LAP12


title: Heads young, P2

description: Library name: D091T05


title: U2OS cells, WT, RNA-seq rep4


title: Guts old, P3

description: Library name: D091T09


title: Heads young, P1

description: Library name: D091T04


title: REN188_B2

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Prime View Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using the “limma”package and R studio version 4.2.2.

label: biotin

source_name: Active/probable ABMR, DSA-positive

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA

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

value: kidney biopsy

tag: time from transplantation in days


title: lung normal tissue 3

description:
Library name: LAP11
LAP11


title: lung normal tissue 2

description:
Library name: LAP10
LAP10


title: U2OS cells, WT, RNA-seq rep3


title: U2OS cells, ZBTB48 KO, RNA-seq rep1


title: U2OS cells, WT, RNA-seq rep2


title: Guts old, P2

description: Library name: D091T08


title: lung normal tissue 1

description:
Library name: LAP1
LAP1


title: primary tumor 25

description:
Library name: C9
C9

value: tumor


title: U2OS cells, WT, RNA-seq rep1


title: Guts old, P1

description: Library name: D091T07


title: U2OS cells, ZBTB48 KO IFNg FAIRE, rep2

data_processing:
Reads were trimmed for adapter sequences using trimmomatic PE v0.39
Mapped to human reference genome (GRCh38) using bowtie2 v2.2.5
Alignments that had a mapping quality less than 30 were removed using samtools v1.14
Peaks were called using MACS 2.2.7.1 and subject to irreproducible discovery rate analysis (IDR 2.0.4.2)
bigwig tracks generated using bamCoverage (deeptools v3.5.1) with cpm normalization
Assembly: GRCh38 (GCA_000001405.15)
Supplementary files format and content: bigwig track for each sample, signal
Supplementary files format and content: narrowpeak file

extract_protocol:
Cells with fixed with 1% formaldehyde for 20mins. After quenching and cell lysis, chromatin was sonicated using an EpiShear Probe Sonicator (Active Motif) at 30% amplitude, 25 cycles of 15s ON/ 30s OFF and phenol chloroform extraction was perfomed to obtained free DNA.
FAIRE-seq library prepared by NovogeneAIT (Singapore)


title: GFPactiveTLR4siRNAHC_35

city: Aachen

first: Matthias

last: Bartneck

address: Pauwelsstraße 30

department: Department of Internal Medicine III

institute: University Hospital RWTH Aachen

data_processing:
FASTQ files were generated using bcl2fastq (Illumina). To facilitate reproducible analysis, samples were processed using the publicly available nf-core/RNA-seq pipeline version 3.12 (Ewels et al. 2020) implemented in Nextflow 23.10.0 (Di Tommaso et al. 2017) with the minimal command and deduplication by UMIs. In brief, lane-level reads were trimmed using Trim Galore 0.6.7 (Krueger et al. 2021) and aligned to the mice genome (GRCm39) using STAR 2.7.9a (Dobin et al. 2013). Gene-level and transcript-level quantification was done by Salmon v1.10.1 (Patro et al. 2017). All analysis was performed using custom scripts in R version 4.3.2 using the DESeq2 v.1.32.0 framework (Love, Huber, and Anders 2014).
Assembly: GRCm39
Supplementary files format and content: Excel file contains the normalized reads for all samples.

source_name: Liver

extract_protocol:
For the isolation of total RNA from cells isolated by fluorescence- activated cell sorting, the RNeasy Plus Micro Kit (Qiagen, 74034), according to manufacturer’s protocol.
3'mRNA sequencing libraries were prepared using Lexogen QuantSeq 3'mRNA-Seq v2 Library Prep Kit FWD with UDIs and the UMI Second Strand Synthesis Module  following the manufacturer's protocol. Prior to library preparation, the concentration of RNA was measured using the Promega Quantus Fluorometer. Additionally, the size distribution of the RNA was assessed using the Agilent TapeStation with an RNA ScreenTape. Quantifiaction and quality assessment were repeated after library preparation, again using the Quantus fluorometer and the Agilent TapeStation with a High Sensitivity D1000 ScreenTape. Libraries were denatured, diluted, and loaded onto a NextSeq High Output v2.5 (75 cycles) flow cell. The 20% PhiX control library was spiked in to improve base calling accuracy. Single-end sequencing was performed with 75 cycles on the Illumina NextSeq platform according to the manufacturer's instructions.

value: Liver

value: Primary cells

value: Hepatocyte

value: Egfp mRNA + Tlr4 siRNA LNP


title: GFPactiveTLR4siRNAHC_36


title: primary tumor 23

description:
Library name: C7
C7


title: primary tumor 24

description:
Library name: C8
C8


title: REN130_B2


title: REN023_B1


title: U2OS cells, WT IFNg FAIRE, rep2


title: GFPactiveTLR4siRNAHC_34


title: U2OS cells, ZBTB48 KO IFng FAIRE, rep1


title: GFPactiveTLR4siRNAHC_32


title: primary tumor 22

description:
Library name: C6
C6


title: GFPactiveTLR4siRNAHC_33


title: primary tumor 20

description:
Library name: C4
C4


title: U2OS cells, ZBTB48 KO FAIRE, rep2


title: REN162_B1

source_name: No-rejection, DSA-positive


title: primary tumor 21

description:
Library name: C5
C5


title: U2OS cells, WT IFNg FAIRE, rep1


title: WT2HC_30

value: Control


title: GFPactiveTLR4siRNAHC_31


title: PRG29_B1


title: REN249_B1


title: REN220_B1


title: REN065_B2


title: primary tumor 18

description:
Library name: C29
C29


title: primary tumor 19

description:
Library name: C3
C3


title: U2OS cells, WT FAIRE, rep2


title: REN225_B1


title: WT2HC_29


title: primary tumor 16

description:
Library name: C27
C27


title: U2OS cells, ZBTB48 KO FAIRE, rep1

value: ZBTB48 Knockout


title: REN093_B1


title: primary tumor 14

description:
Library name: C25
C25


title: primary tumor 13

description:
Library name: C24
C24


title: primary tumor 17

description:
Library name: C28
C28


title: REN213_B1


title: WT2HC_26


title: U2OS cells, WT FAIRE, rep1


title: WT2HC_28


title: U2OS cells, ZBTB48 KO H3K4me3 ChIP, rep1

data_processing:
Reads were trimmed for adapter sequences using trimmomatic PE v0.39
Aligned to the human reference genome version GRCh38 using bowtie2 version 2.3.5.1
Multimapping, unmapped and duplicate reads were removed uisng sambamba version 1.0
Peaks were called using MACS version 2.1.1.2 in paired-end mode with default q‐value cut‐off and --broad flag
Quantitative differential binding analysis with Diffbind 3.2.1
bigwig tracks generated using bamCoverage (deeptools v3.5.0) with cpm normalization
Assembly: GRCh38 (GCA_000001405.15)
Supplementary files format and content: bigwig track for each sample, signal
Supplementary files format and content: broadpeak file, except input

extract_protocol:
Cells with fixed with 1% formaldehyde for 20mins. After quenching and cell lysis, chromatin was sheared to 200-400bp by sonication using an EpiShear Probe Sonicator (Active Motif) at 30% amplitude, 25 cycles of 15s ON/ 30s OFF
ChIP-seq library prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

tag: chip antibody


title: U2OS cells, WT input, rep2


title: U2OS cells, ZBTB48 KO IFNg, RNA-seq rep2

value: IFNg


title: primary tumor 15

description:
Library name: C26
C26


title: lung normal tissue 19

description:
Library name: LAP9
LAP9


title: U2OS cells, WT input, rep1

value: WT


title: GFPactiveTLR4siRNA_22

value: Kupffer cell


title: GFPactiveTLR4siRNA_23


title: WT2HC_25


title: U2OS cells, ZBTB48 KO H3K4me3 ChIP, rep3


title: U2OS cells, WT H3K4me3 ChIP, rep2


title: REN227_B1


title: WT2HC_27


title: WT2_21


title: primary tumor 9

description:
Library name: C18
C18


title: GFPactiveTLR4siRNA_24


title: U2OS cells, WT H3K4me3 ChIP, rep1


title: REN084_B1


title: primary tumor 12

description:
Library name: C23
C23


title: U2OS cells, ZBTB48 KO H3K4me3 ChIP, rep2


title: WT2_20


title: primary tumor 8

description:
Library name: C16
C16


title: primary tumor 11

description:
Library name: C2
C2


title: REN154_B1


title: WT2_19


title: U2OS cells, WT H3K4me3 ChIP, rep3


title: primary tumor 6

description:
Library name: C14
C14


title: REN239_B1

source_name: No-rejection, DSA-negative


title: primary tumor 10

description:
Library name: C19
C19


title: REN173_B1


title: REN230_B1


title: REN100_B1


title: REN215_B1


title: REN172_B1


title: REN061_B1


title: REN186_B1


title: REN034_B1


title: REN248_B1


title: primary tumor 7

description:
Library name: C15
C15


title: GFPactiveTLR4siRNA_18


title: GFPactiveTLR4siRNA_16


title: primary tumor 5

description:
Library name: C13
C13


title: GFPactiveTLR4siRNA_17


title: primary tumor 4

description:
Library name: C12
C12