title: mtC_12WRec_K4me1_Cut&Tag_Rep6

city: New York

first: Rohit

last: Chandwani

state: NY

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

data_processing:
*library strategy: CUT&Tag
Raw sequencing reads trimmed with fastp (Chen et al., 2018) and then processed using the nf-core/cutandrun v3.0 pipeline (10.5281/zenodo.5653535). Peak calling was performed using SEACR (Meers et al., 2019).  The following following parameters were used: --dedup_target_reads --normalisation_mode BPM --normalisation_binsize 50 --peakcaller seacr --seacr_peak_threshold 0.05 --seacr_norm norm.
Assembly: mm9
Supplementary files format and content: BigWig files and SEACR peaks in bed format

source_name: Pancreas

extract_protocol:
nuclear extraction and immunopurification
pA-Tn5 CUT&Tag

treatment_protocol: caerulein-induced pancreatitis

value: Pancreas

value: Acinar

value: Wildtype

value: Caerulein

tag: time point

value: 12 weeks recovery


title: WT+GFP+Asc_rep1

status: Public on Dec 19 2023

type: SRA

city: Cambridge

first: Matthew

middle: D

last: Shoulders

state: MA

address: 77 Massachusetts Avenue

department: Chemistry

country: USA

institute: Massachusetts Institute of Technology

description: Data were sequenced as paired-end but are submitted as single-end data. The first read only contains read and sample barcodes. Before any analysis is performed, the sequence from read 1 is concatenated with the header of read#2  and the fastq files are handled as SE RNA-Seq data.

library_source: transcriptomic

data_processing:
Post-sequencing, quality-control on each of the libraries was performed to assess coverage depth, enrichment for messenger RNA (exon/intron and exon/intergenic density ratios), fraction of rRNA reads and number of detected genes using bespoke scripts.
Read pairs were combined into a single fastq with well/UMI information concatenated with the second read name, reads sharing sequence and UMI information were collapsed into single exemplars. Sequences were aligned against the human genome GRCh38/hg38 ENSEMBL 89 using STAR, with parameters --runThreadN 8 --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM, pointing to a Suffix Array assembly containing exon-exon junctions for 75 nucleotide reads.
Gene expression was estimated based on reads mapping near the 3' end of transcripts using ESAT [Derr2016] with the following parameters -task score3p -alignments $sample_list   -wLen 50 -wExt 5000 -wOlap 0 -sigTest 0.01 -multimap ignore, poiting to a refseq-based gene annotation (hg38, as downloaded from the UCSC Genome Browser) and gene-level data were used for downstream analyses.
Genome_build: GRCh38/hg38 ENSEMBL 89
Supplementary_files_format_and_content: ESAT gene by sample count matrices

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: 1.0×10^5 cells were plated in a 6-well plate.

extract_protocol:
Cells were harvested by trypsinization, washed with PBS, and total RNA was extracted using the Omega RNA Purification Kit.
RNA samples were quantified and quality assessed using an Advanced Analytical Fragment Analyzer. The initial steps were performed on a Tecan EVO150.10ng of totalRNA was used for library. 3’DGE-custom primers were added to a final concentration of 1 uM.   Maxima H Minus RT was then added per manufacturer’s recommendations with Template-Switching oligo5V6NEXT followed by incubation at 42C for 90’ and inactivation at 80C for 10’. cDNA from 12 wells containing unique well identifiers were pooled together and cleaned using RNA Ampure beads at 1.0X. cDNA was eluted with 17 ul of water followed by digestion with Exonuclease I at 37C for 30 minutes, inactivation at 80C for 20 minutes.  Second strand synthesis and PCR amplification was done by adding the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer (10 pmol) directly to the exonuclease reaction. 15 cycles of PCR were performed followed by clean up using regular SPRI beads at 0.6X, and eluted with 20ul of EB. Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries are then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer in place of the normal N500 primer. Final libraries were cleaned using SPRI beads at 0.7X and quantified using the Fragment Analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq500 in paired-end mode (20/50 nt reads).

treatment_protocol: 24 h after the cells were plated, the media was replaced and supplemented with adenoviral supernatant. After 24 h of incubation with virus, the media was replaced with fresh media. 48 h post media change, media was replaced with 1 mL of media supplemented with 200 uM sodium ascorbate. 24 h later, cells were harvested for totalRNA isolation.

tag: cell type

value: adult derived primary fibroblast cells

tag: disease state

value: healthy donor

tag: treatment

value: GFP Adenovirus ; 24 h 200 uM sodium ascorbate


title: DU14-03S0000944_S45

city: Durham

first: Emily

middle: R.

last: Ko

state: NC

address: 4103 Graceview Way

department: Medicine

institute: Duke University

data_processing:
Batch 1 was sequenced on an Illumina HiSeq 2500, and batch 2 was sequenced on an Illumina NovaSeq 6000.
For batch 1, adapters were removed by EA Genomics prior to receipt of sequences.  For batch 2, adapters were remvoed using Trimmomatic v0.38.
Reads were aligned to the hg38 reference transcriptome using Bowtie2 with "option --very-sensitive-local"
Express version 1.5.1 was used for quantification at the transcript level. For batch 1 the option "strand rf-stranded" was used, and for batch 2 "strand fr-stranded" was used.
Expression data were normalized using the trimmed mean of M-values approach, specifically using the calcNormFactors function in the edgeR package in R.
Supplementary files format and content: The processed data file contains log2-transformed and normalized counts per million.

molecule: total RNA

source_name: whole blood

extract_protocol:
Total RNA was extracted from whole blood collected and stored at -80°C in PAXgene Blood RNA tubes using the PAXgene miRNA Extraction Kit
For batch 1, libraries were constructed using GlobinClear Globin RNA Reduction (Invitrogen) with TruSeq Stranded mRNA Library Kit (Illumina).  For batch 2, libraries were contructed using NuGEN Universal Plus mRNA-Seq Library Prep Kit with AnyDeplete Globin depletion (NuGEN/Tecan).

tag: sequencing batch

tag: gender

value: female

tag: age

tag: race

tag: site

tag: infection type

value: Noninfection

tag: pathogen


title: DU14-03S0000942_S43


title: mtC_12WRec_K27ac_Cut&Tag_Rep6

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: genotype


title: DU14-03S0000941_S42

value: male

value: White


title: mtS_12WRec_K27me3_Cut&Tag_Rep4

value: Saline


title: DU14-03S0000940_S23

value: Bacterial

value: Enterobacter


title: CML 2 NDC 72 HRS

city: Glasgow

first: David

last: Vetrie

address: Wolfson Wohl Cancer Research Centre

department: Institute of Cancer Sciences

country: United Kingdom

institute: Glasgow University

data_processing:
Raw sequencing data was pre-processed using the University of Glasgow Galaxy server (https://www.polyomics.gla.ac.uk/galaxy.html) for which quality control was performed by FastQC (0.72) and the reads were trimmed by Trim Galore! (0.4.3.1). Trimmed reads were aligned to human reference genome hg38 using HISAT2 (2.1.0) and assigned by the feature counting tool featureCount (1.6.0.3). Differentially expressed genes between experimental conditions were obtained by DESeq2 (1.32.0) in R.
Assembly: human reference genome GRCh38/hg38
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

source_name: peripheral blood

growth_protocol: CML CD34+ cells were cultured for up to 72 hrs at 37oC in serum free media (20% BIT, 100 μM β-mercaptoethanol, 0.04 mg/mL low density lipoprotein, 2 mM L-glutamine and 1% penicillin-streptomycin in IMDM) containing physiological levels of growth factors (SCF 0.2ng/mL, G-CSF 1ng/mL, GM-CSF 0.2ng/mL, IL-6 1ng/mL, LIF 0.05ng/mL, MIP-α 0.2ng/mL, StemCell Technologies).

extract_protocol:
The cells were pelleted by centrifugation in culture media, washed and then pelleted again in phosphate buffered saline pH 7.4, and total cellular RNA extracted from a minimum of 1 x106 cells in TRIzoLTM Reagent (ThermoFisher). The concentration of the RNA was measured using the Nanodrop 2000, and the quality and RIN value was determined using the Agilent Bioanalyser RNA Nano kit (Agilent).
RNA-seq libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) with single indexing following the manufacturers’ instructions. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: Primary CD34+ CML cells were treated with nilotinib (3 µM), idasanutlin (166 nM), or a combination for 24 hr or 72 hr.

value: peripheral blood

value: CD34+ stem/progenitor cells

value: CML chronic phase diagnosis

value: no drug treatment

tag: time

value: 72 hrs

tag: Sex

value: F


title: CML 1 NIL+IDASA 72 HRS

value: nilotinib + idasanutlin


title: mtS_12WRec_K4me1_Cut&Tag_Rep3

value: Pancreas

value: Acinar

value: Wildtype

value: 12 weeks recovery


title: CML 2 IDASA 72 HRS

value: idasanutlin


title: DU14-03S0000939_S22

value: female

value: Noninfection


title: CML 2 NIL 72 HRS

value: nilotinib


title: CML 2 NIL+IDASA 72 HRS


title: CML 1 NIL 72 HRS


title: mtC_12WRec_K4me1_Cut&Tag_Rep5

value: Caerulein


title: mtS_12WRec_K27ac_Cut&Tag_Rep4

value: Saline


title: DU14-03S0000938_S21

value: male

value: White


title: CML 1 NDC 72 HRS

value: peripheral blood

value: CD34+ stem/progenitor cells

value: CML chronic phase diagnosis


title: CML 1 IDASA 72 HRS

value: 72 hrs

value: F


title: mtC_12WRec_K27me3_Cut&Tag_Rep4

value: Pancreas


title: DU14-03S0000937_S20


title: DU14-03S0000936_S7


title: CML 3 NIL 24 HRS

value: 24 hrs

value: M


title: CML 3 NIL+IDASA 24 HRS

value: nilotinib + idasanutlin


title: mtC_12WRec_K4me1_Cut&Tag_Rep4

value: Acinar

value: Wildtype

value: 12 weeks recovery


title: DU14-03S0000935_S6

value: female

value: Noninfection


title: CML 3 IDASA 24 HRS

value: idasanutlin


title: DU14-03S0000934_S5


title: CML 3 NDC 24 HRS

value: no drug treatment


title: Shox2, replicate 2, ChIP-seq

city: HOUSTON

first: Zhongming

last: Zhao

state: Texas

address: 7000 Fannin St

department: School of Biomedical Informatics

institute: UTHealth

data_processing:
The raw FASTQ datasets were preprocessed using FastQC (version 0.12.1) and mapped to the mouse genome (mm10) using the Bowtie2 alignment algorithm (version 2.5.1). The resulting alignment files were then used as input for MACS2 (version 2.2.9.1) to call peaks with a p-value threshold of 0.01. Subsequently, the generated bed files were then converted to bigwig files and visualized using Integrative Genomics Viewer (IGV). Likelihood of overlap was quantified by calculating the rate of peaks falling within 5kb of the transcription start site of genes up-regulated at the start of anterior and middle of posterior trajectories.
Assembly: mm10
Supplementary files format and content: bigwig file: a binary file containing called peaks and signal

source_name: Anterior palate

extract_protocol:
The anterior (n=2) and posterior (n=2) 1/3 palatal shelves of E14.0 C57BL/6J mice were microdissected, isolated, and then subjected to ChIP-seq with either SHOX2 antibody (JK-6E) (sc-81955, Santa Cruz), MEOX2 Antibody (A-8) (Sc-376748, Santa Cruz), or normal rabbit IgG (2729, Cell Signaling Technology) as a negative control.
The ChIP assays were performed according to the manufacture’s instruction using SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (9003, CST). Two independent ChIPs were conducted for library generation for each group.

value: Anterior palate

tag: strain

tag: developmental stage

tag: chip-seq antibody


title: Meox2, replicate 1, ChIP-seq

description: SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) (9003, CST)

source_name: Posterior palate

value: Posterior palate

value: MEOX2 Antibody (A-8) (Sc-376748, Santa Cruz)


title: mtS_12WRec_K4me1_Cut&Tag_Rep2

tag: cell type

value: Saline

tag: time point


title: Shox2, replicate 1, ChIP-seq

value: embryonic day (E) 14.0

value: SHOX2 antibody (JK-6E) (sc-81955, Santa Cruz)


title: mtS_12WRec_K27me3_Cut&Tag_Rep3

value: Pancreas

tag: treatment


title: DU10-01S0000099_S61

tag: sequencing batch

value: male

value: White

value: Bacterial

value: Streptococcus


title: DU10-01S0000100_S56

tag: gender

value: Viral


title: mtS_12WRec_K27ac_Cut&Tag_Rep3

value: Acinar

value: Wildtype

value: 12 weeks recovery


title: mtS_12WRec_K27ac_Cut&Tag_Rep2


title: DU10-01S0000017_S9

tag: age

value: Enterobacter


title: mtC_12WRec_K4me1_Cut&Tag_Rep3

value: Caerulein


title: Meox2, replicate 2, ChIP-seq


title: DU10-01S0000030_S25

value: female

tag: race


title: DU10-01S0000012_S24

tag: site


title: mtC_12WRec_K27ac_Cut&Tag_Rep5


title: DU10-01S0000002_S26

tag: infection type

value: Staphylococcus


title: CML 1 NIL 24 HRS

value: peripheral blood

value: CD34+ stem/progenitor cells

tag: disease state

value: CML chronic phase diagnosis

value: nilotinib

value: 24 hrs

value: F


title: CML 1 NIL+IDASA 24 HRS

tag: tissue

value: nilotinib + idasanutlin


title: mtC_12WRec_K27me3_Cut&Tag_Rep3

value: Pancreas

tag: genotype


title: CML 2 NDC 24 HRS

value: no drug treatment

tag: time


title: CML 2 IDASA 24 HRS

value: idasanutlin

tag: Sex


title: CML 2 NIL+IDASA 24 HRS


title: DU09-03S96913_S39

value: White

value: Viral

tag: pathogen


title: CML 1 IDASA 24 HRS


title: mtC_12WRec_K27ac_Cut&Tag_Rep3

value: Acinar

value: Wildtype

value: 12 weeks recovery


title: CML 1 NDC 24 HRS


title: DU09-03S0000129_S11

value: male


title: mtC_12WRec_IgG_Cut&Tag_Rep1

value: Caerulein


title: BV173 + IDASA input

data_processing:
Raw sequencing data was pre-processed using the University of Glasgow Galaxy server (https://www.polyomics.gla.ac.uk/galaxy.html) for which quality control was performed by FastQC (0.72) and the reads were trimmed by Trim Galore! (0.4.3.1). For p53 ChIP-sequencing and input sample, the trimmed reads were aligned to human reference genome hg38 using Bowtie2 (2.3.4.2). Narrow peaks were called by MACS2 (2.2.7.1) with q value 0.05. Gene annotation of p53 ChIP-seq peaks employed ChIPseeker (1.28.3) (in R 3.6.3) with the annotation database TxDb.Hsapiens.UCSC.hg38.knownGene.
Assembly: human reference genome GRCh38/hg38
Supplementary files format and content: Comma-seperated values file containing annotated peaks from ChIPseeker (except for Input samples)
Supplementary files format and content: BED (except for Input samples)

source_name: BV173 cell line

growth_protocol: The BV173 cell line was cultured at 37oC in RPMI 1640 media (Sigma) supplemented with 20% fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine and 1% (v/v) penicillin-streptomycin.

extract_protocol:
1 x 10^7 BV173 cells were pelleted by centrifugation and resuspended in FBS-free RPMI media and cross-linked by adding methanol-free paraformaldehyde (VWR; final conc. 1%) for 15 min with gentle stirring. Cross-linking was quenched by adding glycine [0.125M]. Cells were then pelleted by centrifugation, washed in PBS and pelleted again. Cells were resuspended in ∼1.5 x pellet volume of cell lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630; protease inhibitors) and incubated for 10 min on ice. The cell nuclei were pelleted by centrifugation at 2500 rpm for 5 min at 4°C and resuspended in 1.2 mL of nuclear lysis buffer (NLB 50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, protease inhibitors) and incubated on ice for 10 min. Volume was increased to 2 mL by adding 0.72 mL of immunoprecipitation (IP) dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA 1% Triton X-100, 0.01% SDS, protease inhibitors) and the chromatin was transferred to a 5 mL tube (Falcon) and sheared to a fragment size of 200-500 bp by sonication (Soniprep 150, MSE). The sheared chromatin was diluted with 4.1 mL of IP dilution buffer and pre-cleared by adding 10 μg rabbit IgG (12-370, Millipore) for 1 hr followed by incubation with 200 μL of protein G-agarose bead suspension (Roche) for 3 hr. The protein G-agarose beads were removed by brief centrifugation and 1.35 mL of the chromatin was added to 10 μg of p53 antibody (DO-1, sc-126, Santa Cruz Biotechnology) for overnight incubation. ChIP was carried out by adding 100 μL protein G-agarose beads suspension for 3 hr. Beads were washed (twice in 20 mM Tris-HCl pH 8.1, 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS; once in 10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% IGEPAL CA630, 1% deoxycholic acid; twice in 10 mM Tris-HCl 1 mM EDTA pH 8.0). The immune complexes were eluted from the beads (twice in 225 μL of 100 mM NaHCO3, 0.1% SDS). Crosslinks were reversed by adding 0.2 μL of RNase A (10 mg/mL, ICN) and 27 μL of 5 M NaCl to the eluates with incubation at 65°C for 6 hr and then overnight at 45oC in the presence of 90 μg proteinase K (Invitrogen). DNA was purified by phenol chloroform extraction followed by ethanol precipitation and resuspension in 50 μL of water.
ChIP-sequencing libraries were generated using the Nextera XT DNA Library Preparation Kit (Illumina) with dual indexing (Nextera XT Index Kit, Illumina) following manufacturers’ instructions.  Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: BV173 cells were cultured for 6 hrs with and without idasanutlin (300 nM in DMSO).

tag: cell line

value: BV173 cell line

value: B cell precursor leukemia

value: CML lymphoid blast crisis

value: wild type p53

tag: chip antibody


title: DU09-03S0000128_S29

value: female


title: CML 2 NIL 24 HRS

value: peripheral blood

tag: cell type

value: CD34+ stem/progenitor cells

value: CML chronic phase diagnosis

value: nilotinib

value: 24 hrs

value: F


title: mtC_12WRec_K27ac_Cut&Tag_Rep4

value: Pancreas

tag: time point


title: mtS_12WRec_K4me1_Cut&Tag_Rep1

value: Acinar

tag: treatment

value: Saline


title: BV173 - IDASA input

value: no drug control


title: DU09-03S0000127_S28

tag: sequencing batch

value: White

value: Noninfection


title: mtS_12WRec_K27me3_Cut&Tag_Rep2

value: Wildtype

value: 12 weeks recovery


title: DU09-03S0000126_S16

tag: gender

value: male


title: BV173 + IDASA p53 ChiP

value: BV173 cell line

value: B cell precursor leukemia

value: CML lymphoid blast crisis

value: wild type p53

value: idasanutlin

value: anti-p53 (DO-1) Santa Cruz sc-126


title: DU09-03S0000125_S15

tag: age

value: Bacterial

value: Streptococcus


title: BV173 - IDASA p53 ChIP


title: mtC_12WRec_K4me1_Cut&Tag_Rep2

value: Pancreas

value: Caerulein


title: mtC_12WRec_K27me3_Cut&Tag_Rep2

value: Acinar


title: 7-day old βNrf2KO mouse 4

city: Duarte

first: Sharon

last: Baumel Alterzon

state: California

address: 1500 East Duarte road

department: Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute

institute: City of Hope

data_processing:
Raw sequence data were converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software with one mismatch allowed for index sequence identification.
After demultiplexing and quality and yield checking, raw reads were trimmed to remove adapter sequences and poor-quality readings using Trimmomatic (version 0.36).
The reads were then mapped to the ENSEMBL Mus musculus GRcm39/mm39 reference genome using STAR aligner (version 2.5.2b).
BAM files were generated, and unique gene hit counts were calculated by using feature Counts from the Subread package (version 1.5.2). Unique reads that fell within exon regions were counted.
Assembly: GRcm39/mm39
Supplementary files format and content: tab delimited text files include raw counts for each sample
Supplementary files format and content: tab delimited text file include raw count for all samples

source_name: Pancreatic Islets

extract_protocol:
Total RNA was extracted from islets isolated from 7-day old mice using the RNeasy Micro Kit (QIAGEN, Germantown, MD, USA).
rRNA depletion libraries were prepared using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany) and NEBNext Ultra II RNA Library Preparation Kit for Illumina HiSeq (NEB, Ipswich, MA, USA), following the manufacturer’s recommendations.

treatment_protocol: Given the limited amount of RNA retrievable from each sample, RNA pools were generated, each by using RNA extracted from 5 animals, totaling 7 samples.

value: Pancreatic Islets

value: beta-cell specific Nrf2 deletion


title: DU09-03S0000124_S13

tag: race

value: Noninfection


title: mtC_12WRec_K27ac_Cut&Tag_Rep2

value: Wildtype


title: DU09-03S0000123_S14

value: female

value: White

tag: site

value: Enterobacter


title: mtS_12WRec_K27me3_Cut&Tag_Rep1

value: Saline

value: 12 weeks recovery


title: OD1_1

city: Würzburg

first: Yanying

last: Yu

state: DE Deutschland

address: Josef-Schneider-Str. 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Library strategy: DNA-seq
Paired-end reads were merged using BBMerge (version 38.69) with parameters “qtrim2=t, ecco, trimq=20, -Xmx1g”
Sequence reads with perfect matches were assigned to the gRNA library using a Python script
After filtering by 1 count per million in minimal 4 samples, read counts of each gRNA were normalized by scale factors determined from non-targeting guides using the trimmed mean of M-values method in edgeR (version 3.28.0). An extra column was added to the design matrix to account for batch effects between the two cultures. Differential abundance (logFC) of gRNAs between time points and that of the input library were calculated using a quasi-likelihood F test after fitting a generalized linear model.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: CSV, normalized differential abundance of each gRNA in different time points

organism: Escherichia coli

source_name: Escherichia coli MG1658

growth_protocol: E. coli strain MG1655 was initially transformed with a dCas9 encoding plasmid (2.0 kV, 200 Omega, and 25 μF). The resulting strain SG332 was transformed with the sgRNA library by electroporation and recovered in 900 µl SOC for 1.5h at 37 °C with shaking at 250 rpm. Different dilutions of the recovered cells were plated on Luria Bertani (LB) agar containing the 34 µg/mL chloramphenicol and incubated for 16 h to check the number of the resulting colonies (~56^5 colonies). The recovered culture was back-diluted to OD600 0.01 in LB medium (10 g/L NaCl, 5 g/L yeast extract, 10 g/L tryptone) with 34 µg/mL chloramphenicol and incubated at  37 °C with shaking for 13h.

extract_protocol:
5 mL of the culture was sampled before (as input) and after being incubated in M9 minimal medium (at OD600 0.2, 0.6 and 1). The plasmids were extracted by miniprep (Nucleospin Plasmid, Macherey-Nagel).
The sequencing library was generated using the KAPA HiFi HotStart Library Amplification Kit for Illumina® platforms (Roche)

treatment_protocol: The culture grown in LB  was sampled and washed twice with M9 minimal medium to remove traces of the LB medium, to reach OD600 0.01 in 50 ml M9 minimal medium (1x M9 salts, 1 mM thiamine hydrochloride, 0.4% glucose, 0.2% casamino acids, 2 mM MgSO4, 0.1 mM CaCl2). The culture was incubated at 37°C with shaking until it reached OD600 1, allowing ~6 replications.

tag: strain

value: MG1655 transformed with pCB456

value: M9 minimal medium


title: OD1_2


title: DU09-03S0000121_S32

value: male

tag: infection type


title: OD06_2

source_name: Escherichia coli MG1657

value: MG1655 transformed with pCB455


title: 7-day old βNrf2KO mouse 2

tag: tissue


title: mtS_12WRec_K27ac_Cut&Tag_Rep1

tag: genotype


title: OD06_1


title: mtC_12WRec_K4me1_Cut&Tag_Rep1


title: 7-day old NRF2lox/lox mouse 4


title: DU09-03S0000119_S60


title: PRP_difer6w_3

type: RNA

city: Valencia

first: Rubén

last: Salvador-Clavell

state: Valencia

address: 13 Blasco Ibanez Av.

country: Spain

institute: University of Valencia

description: microRNA expression data from pBM-MSC gelatin-PRP microspheres in chondrogenic differentiation medium for 6 weeks of culture

hyb_protocol: The biotinylated RNA were hybridized with the microarrays in a 645-hybridization oven (Affymetrix, CA, USA), following standardized protocols provided by Affymetrix.

scan_protocol: The samples were performed using a Fluidic 450 Station and a GeneChip 3000 7G confocal scanner (Affymetrix, CA, USA).

data_processing: MicroRNA expressions were analyzed using Transcriptome Analysis Console (TAC) Software (Applied Biosystems).

label: biotin

organism: Sus scrofa

source_name: pBM-MSC gelatin-PRP microspheres in chondrogenic differentiation medium for 6 weeks of culture, biological rep 3

label_protocol: The miRNA extracts were labeled with biotin, using 3DNA Array Detection FlashTag™ Biotin HSR (Genisphere, Hatfield, USA) following standardized protocols provided by Affymetrix.

growth_protocol: Cultures were maintained for 6 weeks at 37 ºC and 5% CO2.

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

treatment_protocol: Cells were seeded in gelatin or gelatin-PRP microspheres and cultured with proliferation and chondrogenic differentiation media (Gibco).

value: Sus scrofa Bone Marrow Mesenchymal Stem Cells

tag: material

value: gelatin-PRP

tag: culture media

value: chondrogenic differentiation

tag: culture time

value: 6 weeks


title: 7-day old βNrf2KO mouse 3

value: Pancreatic Islets


title: OD02_2

source_name: Escherichia coli MG1656

value: MG1655 transformed with pCB454


title: 7-day old NRF2lox/lox mouse 2


title: DU09-03S0000033_S17

value: Noninfection

tag: pathogen


title: 8394_S40

value: Bacterial


title: 7-day old NRF2lox/lox mouse 1


title: mtC_12WRec_K27ac_Cut&Tag_Rep1

value: Pancreas

value: Acinar

value: Wildtype

value: Caerulein


title: 7-day old βNrf2KO mouse 1

value: beta-cell specific Nrf2 deletion


title: mtC_K4me1_CP_2DRec_Cut&Tag_Rep2

value: 2 days recovery


title: DU09-03S0000120_S20

value: female


title: 413968_S33

value: male

value: White

value: Viral


title: mtC_12WRec_K27me3_Cut&Tag_Rep1

value: 12 weeks recovery


title: mtC_K27me3_CP_2DRec_Cut&Tag_Rep2


title: GEL_proli6w_3

description: microRNA expression data from pBM-MSC gelatin microspheres in proliferation medium for 6 weeks of culture

source_name: pBM-MSC gelatin microspheres in proliferation medium for 6 weeks of culture, biological rep 3

value: Sus scrofa Bone Marrow Mesenchymal Stem Cells

value: gelatin

value: proliferation


title: 352105_S7


title: mtC_K27ac_CP_2DRec_Cut&Tag_Rep2


title: GEL_difer6w_3

description: microRNA expression data from pBM-MSC gelatin microspheres in chondrogenic differentiation medium for 6 weeks of culture

source_name: pBM-MSC gelatin microspheres in chondrogenic differentiation medium for 6 weeks of culture, biological rep 3

value: chondrogenic differentiation

value: 6 weeks


title: 348339_S6

value: Bacterial

value: Streptococcus


title: 286678_S37

value: Noninfection


title: mtS_K4me1_CP_2DRec_Cut&Tag_Rep2

value: Pancreas

value: Acinar

value: Wildtype

value: Saline


title: 286671_S5


title: mtS_K27me3_CP_2DRec_Cut&Tag_Rep2

value: 2 days recovery


title: SB525334_KN046_3

city: Shanghai

first: Jiwei

last: Chen

address: 130 DongAn Road

country: China

institute: Fudan University

data_processing:
Cutadapt (v2.7) software was used to filter the sequencing data to obtain a high-quality sequence (Clean Data) for further analysis. The clean reads were aligned to mouse GRCm39 genome assembly (v108.39) using HISAT2 (v2.2.1). Gene expression quantification was performed with HTSeq (v2.0.4). Normalization and Differential expression analysis was performed using R package DESeq2 (v1.38.3).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw and normalized Count values for each Sample

source_name: liver metastases

growth_protocol: Six-week-old male wild-type (WT) C57BL/6 mice were housed in a pathogen-free facility.

extract_protocol:
Total RNA was extracted from tumor tissues of mice with liver metastases.
Total RNA samples were then submitted to Shanghai Bioprofile Co., Ltd. (Shanghai, China) for preparation and construction of the mRNA library, followed by transcriptomic sequencing on the HiSeq X Ten System (Illumina, San Diego, CA, USA).

treatment_protocol: For the liver metastasis of CRC models, the MC-38 cells (2×105 cells) suspended in 40 μl PBS were injected into the inferior hemispleen into each 6-week-old C57/BL6 mouse. KN046 (Alphamab Oncology, Suzhou, Jiangsu, China) was injected intraperitoneally at a dose of 10 mg/kg twice a week. The TGFβ receptor I (ALK5) inhibitor SB525334 (Selleckchem) dissolved in CMC-Na at 20 mg/kg dose by oral gavage daily.

value: liver metastases

tag: host strain

tag: injected cell_line

tag: injected cell_type

value: Colon Adenocarcinoma Cell


title: SB525334_KN046_1

tag: treatment


title: SB525334_KN046_2


title: OD02_1

value: MG1655 transformed with pCB454

value: M9 minimal medium


title: Input_2

source_name: Escherichia coli MG1655

value: MG1655 transformed with pCB453

value: untreated


title: Input_1


title: SB525334_KN046_4


title: 286615_S36

tag: sequencing batch

value: female

value: White


title: mtC_IgG_CP_2DRec_Cut&Tag_Rep2

tag: cell type

value: Caerulein

tag: time point


title: mtS_K27ac_CP_2DRec_Cut&Tag_Rep2


title: PRP_proli6w_1

description: microRNA expression data from pBM-MSC gelatin-PRP microspheres in proliferation medium for 6 weeks of culture

source_name: pBM-MSC gelatin-PRP microspheres in proliferation medium for 6 weeks of culture, biological rep 1

value: Sus scrofa Bone Marrow Mesenchymal Stem Cells

value: gelatin-PRP

value: proliferation

value: 6 weeks


title: CML 2wk 3

data_processing:
Raw sequencing data was pre-processed using the University of Glasgow Galaxy HPC for which quality control was performed by FastQC (0.11.9) and the reads were trimmed by fastp (0.23.2). Trimmed reads were aligned to mouse reference genome mm39 using STAR (2.7.10a) and assigned by the feature counting tool featureCounts (2.0.1). Differentially expressed genes between experimental conditions were obtained by DESeq2 (1.36.0) in R.
Assembly: mouse reference genome GRCm39/mm39
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

source_name: bone marrow

growth_protocol: Eight to twelve week old B6.SJL recipient mice (CD45.1) were irradiated with two doses of 4.25Gy, 3hrs apart and transplanted with 2 x 106 SCLtTA/BCR-ABL (DTG) mouse BM cells (CD45.2) via tail vein injection. Tetracycline (TET) was included in the drinking water for two weeks post-transplant to allow time for recovery and engraftment. Two weeks post irradiation, TET was removed for two weeks in one cohort, allowing BCR-ABL1 expression and leukaemia development (CML group), while TET administration was continued In a second cohort (CTRL group).

extract_protocol:
Murine CD45.2+Lin-Sca+Kit+ were isolated from the BM of recipient mice by flow sorting (BD FACSAriaTM Fusion) and total cellular RNA extracted using the RNAeasy Mini Kit Plus (QIAGEN).
RNA-seq libraries were prepared using the Kapa RNA HyperPrep kit (Roche) with single indexing following the manufacturers’ instructions. Libraries were quantified using the Agilent Bioanalyzer High Sensitivity DNA Kit.

treatment_protocol: Mice were treated with tetracycline to suppress BCR-ABL1 expression in the recipient mice.

value: bone marrow

value: Lin-Sca+Kit+

tag: disease state

value: CML; leukemia

value: TET off

tag: age

value: 8-12 weeks

tag: Sex

value: Female


title: CML 2wk 4


title: CML 2wk 1


title: CML 2wk 2


title: CML 2wk 6


title: CML 2wk 5


title: KN046_4

value: liver metastases

value: Colon Adenocarcinoma Cell


title: CTRL 6

value: normal

value: TET on

value: Male


title: 286605_S4

tag: gender

value: female

tag: race

value: White

tag: site

tag: infection type

value: Noninfection


title: mtS_IgG_CP_2DRec_Cut&Tag_Rep2

source_name: Pancreas

tag: tissue

value: Pancreas

value: Acinar

tag: genotype

value: Wildtype

value: Saline

value: 2 days recovery


title: KN046_3


title: 136848_S8

source_name: whole blood

value: male

value: Bacterial

tag: pathogen

value: Streptococcus


title: mtC_K4me1_CP_2DRec_Cut&Tag_Rep1

value: Caerulein


title: KN046_2

value: liver metastases

tag: host strain


title: mtC_K27me3_CP_2DRec_Cut&Tag_Rep1


title: PRP_difer6w_1

source_name: pBM-MSC gelatin-PRP microspheres in chondrogenic differentiation medium for 6 weeks of culture, biological rep 1

value: Sus scrofa Bone Marrow Mesenchymal Stem Cells

tag: material

value: gelatin-PRP

tag: culture media

value: chondrogenic differentiation

tag: culture time

value: 6 weeks


title: KN046_1

tag: injected cell_line

tag: injected cell_type

value: Colon Adenocarcinoma Cell

tag: treatment


title: PRP_difer6w_2

source_name: pBM-MSC gelatin-PRP microspheres in chondrogenic differentiation medium for 6 weeks of culture, biological rep 2

tag: cell type


title: NuclearExtract_replicate3_stress_Nab2-Interface mutant

city: Zürich

first: Mostafa

last: Zedan

address: Otto-Stern-Weg 3

country: Switzerland

institute: ETH-Zurich

data_processing:
Reads were adaptor trimmed using cutadapt, mapped to the reference genome using tophat2 after rRNA reads subtraction using botwtie2, and the read counts per gene were quantified using featurecount.
Assembly: The FASTA file of the Yeast Genome was downloaded from the Saccharomyces Genome Database "SGD"
Supplementary files format and content: text file containing the calculated read counts per gene.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in synthetic complete medium with 2% glucose until mid-log phase.

extract_protocol:
1) Whole cell extracts: Cells were harvested and snap-frozen in liquid N2. Pellets were resuspended in lysis buffer and further processed with acid-saturated phenol and chloroform to extract total RNA. Purified RNA was processed with Dynabeads with oligodT(25) for PolyA selection. 2) Nuclear extracts: Cells were spheroplasted with Zymolyase to remove cell walls. Nuclei were released in buffer containing 20% Ficoll and dounced to mechanically assist nucleus release. Nuclei were separated from remaining cell material/debris through sucrose gradient fractionation. The enriched nucleus fraction was resuspended in lysis buffer and further processed with acid-saturated phenol and chloroform to extract total RNA. Purified RNA was processed with Dynabeads with oligodT(25) for PolyA selection.
The eluted poly(A) RNA was used to generate strand-specific sequencing libraries using the NEXTflex Rapid Directional RNA-Seq Library Prep Kit (BioO)

treatment_protocol: Cells were harvested in mid-log phase in medium with glucose (no-stress) or washed 3x in synthetic complete medium without glucose, and cultured for another 24 hrs in synthetic complete medium without glucose before harvesting (stress).

tag: condition

value: stress

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-F450A-GFP-HISMX


title: mtC_K27ac_CP_2DRec_Cut&Tag_Rep1

value: Pancreas

tag: time point


title: NuclearExtract_replicate3_stress_Nab2-wild type

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-yEGFP-HISMX


title: SB525334_3


title: mtS_K4me1_CP_2DRec_Cut&Tag_Rep1

value: Acinar

value: Wildtype


title: GEL_proli6w_2

source_name: pBM-MSC gelatin microspheres in proliferation medium for 6 weeks of culture, biological rep 2

value: gelatin

value: proliferation


title: PRP_proli6w_2

source_name: pBM-MSC gelatin-PRP microspheres in proliferation medium for 6 weeks of culture, biological rep 2


title: GEL_difer6w_2

source_name: pBM-MSC gelatin microspheres in chondrogenic differentiation medium for 6 weeks of culture, biological rep 2


title: NuclearExtract_replicate2_stress_Nab2-Interface mutant


title: GEL_difer6w_1

source_name: pBM-MSC gelatin microspheres in chondrogenic differentiation medium for 6 weeks of culture, biological rep 1


title: PRP_proli6w_3

source_name: pBM-MSC gelatin-PRP microspheres in proliferation medium for 6 weeks of culture, biological rep 3


title: GEL_proli6w_1

source_name: pBM-MSC gelatin microspheres in proliferation medium for 6 weeks of culture, biological rep 1


title: CTRL 2

value: bone marrow

value: Lin-Sca+Kit+

tag: disease state

value: normal

value: TET on

tag: age

value: 8-12 weeks

tag: Sex

value: Male


title: CTRL 4


title: CTRL 1


title: CTRL 5


title: CTRL 3


title: SB525334_2

value: liver metastases


title: TBL3 Cells, MC2646 Treated, Replicate 3

city: Paris

first: Aristeidis

last: Panagiotou

address: 35 Rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

country: France

institute: CNRS

description:
Villares_GSEA.zip
dea_Villares_TBL3_TBL3_2646.tsv

data_processing:
Trimming reads with TrimGalore!
Alignment on concatenated host/parasite genome file with HISAT2
Feature counting with featureCounts ("gene" parameter)
Differential expression analysis between conditions with DESeq2
Geneset enrichment analysis (GSEA)
Assembly: Fused genome and annotation for: Bos taurus: ARS-UCD1.2 Theileria annulata : GCF_000003225.3
Supplementary files format and content: dea_Villares_BL3_TBL3.tsv : Standard DESeq2 output, comparing TBL3 to BL3
Supplementary files format and content: dea_Villares_TBL3_TBL3_2646.tsv : Standard DESeq2 output, comparing MC2646-treated TBL3 to untreated
Supplementary files format and content: dea_Cheeseman_BL3_TBL3.tsv : Based on PRJEB33792, Standard DESeq2 output, comparing TBL3 to BL3
Supplementary files format and content: dea_Cheeseman_TBL3_TBL3_Bup.tsv : Based on PRJEB33792, Standard DESeq2 output, comparing Buparvaquone-treated TBL3 to untreated
Supplementary files format and content: Villares_GSEA.zip : GSEA output reiterating the DESeq2 comparisons

organism: Bos taurus

growth_protocol: All bovine cell lines were previously documented. TBL3 cells were derived from in vitro infection of the spontaneous bovine B lymphosarcoma cell line, BL3, with Hissar stock of T. annulata. Cells were cultured in RPMI 1640 (Gibco-BRL), supplemented with 10% heat-inactivated foetal bovine serum (FBS), 4 mM L-glutamine, 25mM HEPES, 10 mM β-mercaptoethanol and 100 mg/ml of penicillin/streptomycin in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol:
Total RNA was extracted using a Nucleospin RNA extraction kit (MachereyNagel) following the manufacturer’s protocol. 1 μg of total RNA was  reverse transcribed with Superscript III Reverse transciptase Kit (Invitrogen).
Library preparation for Illumina NextSeq 500

treatment_protocol: Bovine cell lines were treated with compound MC2646 at 4 μM for 24 hours

tag: cell line

value: WT

tag: agent

value: Theileria annulata MC2646


title: NuclearExtract_replicate2_stress_Nab2-IDRmutant

tag: tissue

value: stress

tag: genotype

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-{delta}QQQP-{delta}RGG({delta}104-263)-SV40NLS-yEGFP-HISMX


title: mtS_K27me3_CP_2DRec_Cut&Tag_Rep1

value: Pancreas

value: Saline

value: 2 days recovery


title: SB525334_1

tag: host strain

value: Colon Adenocarcinoma Cell


title: mtS_K27ac_CP_2DRec_Cut&Tag_Rep1

value: Acinar

value: Wildtype


title: NuclearExtract_replicate3_stress_Nab2-IDRmutant


title: TBL3 Cells, MC2646 Treated, Replicate 2


title: CTRL_4

value: PBS control


title: NuclearExtract_replicate2_stress_Nab2-wild type

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-yEGFP-HISMX


title: SB525334_4


title: mtC_IgG_CP_2DRec_Cut&Tag_Rep1

value: Caerulein


title: TBL3 Cells, MC2646 Treated, Replicate 1


title: mtS_IgG_CP_2DRec_Cut&Tag_Rep1


title: NuclearExtract_replicate1_stress_Nab2-Interface mutant

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-F450A-GFP-HISMX


title: BL3 Cells, MC2646 Treated, Replicate 3


title: NuclearExtract_replicate1_stress_Nab2-IDRmutant


title: FTW-mESCs/FTW-mTSCs/FTW-mXENs Co-culture 2

city: Kunming

first: Mq

last: Peng

state: Yunnan

address: No. 727, Jingming South Road, Chenggong District

institute: Kunming University of Science and Technology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
10X Genomics
Assembly: mm10

source_name: Embryo

extract_protocol:
Mouse blastocysts were collected at E3.5 and the zona pellucida removed by Tyler’s buffer as described previously(Yu et al., 2021). After removing the zona, blastocysts were washed in PBS/PVA two times. Digestion was performed in TrypLE Express for 10 minutes at 37 ℃, and cell clumps were cut up by mouth glass pipettes beginning with a larger size (50 um diameter) to a smaller size (20 um diameter). The totally digestion time was around 40-50 minutes. For the FTW-derive-day 8 outgrowth samples, blastocysts were collected and plated onto MEF-coated plates in FTW medium for 8 days, and then the outgrowth area were picked and dissociated.  For the established FTW cell lines, all the cells were dissociated with TripLE Express for 3-5 minutes at 37 ℃.
Single cell suspensions were diluted at a concentration of 1100 cells/µL in 0.04% bovine serum albumin (BSA)/PBS for loading into 10X Chromium Single Cell G Chips (for mouse blastocysts, all the of the cells were loaded into the chip). Single cell libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v3.1 (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel beads in EMulsion (GEMs) in the GemCode instrument followed by cell lysis and barcoded reverse transcription of RNA, amplification, shearing and 5’ adaptor and sample index attachment. Libraries were sequenced on the Illumina NovaSeq 6000 platform.

value: Embryonic and extra-embryonic cells

value: Embryo

tag: strain


title: CTRL_3

value: liver metastases


title: NuclearExtract_replicate1_stress_Nab2-wild type


title: BL3 Cells, MC2646 Treated, Replicate 2

value: WT


title: FTW-mESCs/FTW-mTSCs/FTW-mXENs Co-culture 1

description: 10x Genomics


title: CTRL_1


title: CTRL_2


title: BL3 Cells, MC2646 Treated, Replicate 1

value: Theileria annulata MC2646


title: TBL3 Cells, Untreated, Replicate 3

description:
Villares_GSEA.zip
dea_Villares_BL3_TBL3.tsv

value: Untreated


title: WholeCell_replicate2_stress_Nab2-Interface mutant

value: stress


title: FTW-mXENs

description: 10x Genomics

value: Extra-embryonic cells


title: FTW-mTSCs

description: 10x Genomics


title: WholeCell_replicate2_no-stress_Nab2-Interface mutant

value: no stress


title: PBAT sample for ISC-BO, replicate 2

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

data_processing:
The BCL (base calls) binary was converted into FASTQ using illumina package bcl2fastq2 (v2.20.0).
Raw sequencing reads from WGBS with PBAT were mapped to the mouse reference genome sequence (mm9) using the Bmap program (http://itolab.med.kyushu-u.ac.jp/BMap/).
Assembly: mm9
Supplementary files format and content: bedgraph

source_name: intestinal crypt

growth_protocol: MEFs were prepared from E13.5 embryos of C57BL/6 mice (Clea) and cultured in MEF medium as described previously (Sekiya & Suzuki, 2011).  Reprogramed cells and cells from adult intestinal crypts were embedded in Matrigel (BD Biosciences) and cultured in mouse intestinal basal medium [advanced DMEM/F-12 (Thermo Fisher Scientific)] with several supplements (Miura & Suzuki, 2017).

extract_protocol:
The genome DNA samples for WGBS were prepared with NucleoSpin Tissue kit (MACHEREY-NAGEL).
All WGBS libraries were prepared using the PBAT protocol from ∼100 ng of genomic DNA without global PCR amplification (Miura et al., 2012; Miura & Ito, 2018).

value: intestinal crypt

value: intestinal stem cell (ISC)

value: wild type

value: 3D culture in matrigel and mouse intestinal basal medium

tag: developmental stage


title: PBAT sample for ISC-BO, replicate 1


title: PBAT sample for iISC-BO, replicate 3

source_name: embryo

value: embryo

value: mouse embryonic fibroblast (MEF)

value: transfected with Foxa3/Cdx2/Gata6/Hnf4a

value: E13.5 embryos


title: WholeCell_replicate2_stress_Nab2-IDRmutant

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-{delta}QQQP-{delta}RGG({delta}104-263)-SV40NLS-yEGFP-HISMX


title: PBAT sample for iISC-BO, replicate 2


title: WholeCell_replicate2_no-stress_Nab2-IDRmutant


title: Blastocyst outgrowth  (day 8)

description: 10x Genomics

value: Embryonic and extra-embryonic cells

value: Embryo


title: FTW-mESCs

description: 10x Genomics

value: Embryonic and cells


title: TBL3 Cells, Untreated, Replicate 1

value: WT


title: BL3 Cells, Untreated, Replicate 3

value: Untreated


title: BL3 Cells, Untreated, Replicate 2


title: WholeCell_replicate2_stress_Nab2-wild type

value: stress

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-yEGFP-HISMX


title: BL3 Cells, Untreated, Replicate 1


title: WholeCell_replicate2_no-stress_Nab2-wild type

value: no stress


title: pooled cardiac Sham Sox9 EC-KO endothelial cells

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

institute: Medizinische Fakultät Mannheim

data_processing:
The reads were mapped to the reference genome mm10 (version 3.0.0). Analysis was conducted using the Seurat package (version 4.0.2) in R (version 4.0.5).
Data were filtered for cells expressing at least 200 genes and less than 25% mitochondrial counts before the matrix was log-normalized and scaled
Genome_build: mm10

source_name: isolated cardiac endothelial cells

growth_protocol: Sox9fl/fl mice were crossed with Cdh5-Cre+/- and interbred homozygous for Sox9fl/fl and hemizygous for Cre

extract_protocol:
Total RNA was isolated using 10x Genomics Kit
10x Genomics

treatment_protocol: Mice were injected with 0.5 mg Tamoxifen for 5 consecutive days 14 days prior to 1 W TAC or sham operation

value: mixed background

value: heart

value: Sox9 EC-KO


title: PBAT sample for iISC-BO, replicate 1

value: 3D culture in matrigel and mouse intestinal basal medium


title: PBAT sample for MEF, replicate 3

value: embryo

value: wild type

value: 2D culture in MEF medium


title: WholeCell_replicate1_no-stress_Nab2-Interface mutant

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-F450A-GFP-HISMX


title: pooled cardiac Sham WT endothelial cells

value: ctrl


title: WholeCell_replicate1_stress_Nab2-Interface mutant


title: TBL3 Cells, Untreated, Replicate 2


title: pooled cardiac TAC Sox9 EC-KO endothelial cells


title: WholeCell_replicate1_stress_Nab2-IDRmutant

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-{delta}QQQP-{delta}RGG({delta}104-263)-SV40NLS-yEGFP-HISMX


title: CD11b+ cells, LPS4x_3

city: Chuo

first: Kozo

last: Saito

address: 1110 Shimokato

department: Department of Neuropharmacology

institute: University of Yamanashi

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) to remove reads containing sequencing adapter, those with low quality and those with 5% more than unknown base ('N' base) ratio. Clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com/). The clean reads were mapped to the reference genome and reference gene of Mus musculus (UCSC mm39) using HISAT2 (v2.0.4) and Bowtie2 (v2.2.5), respectively. After that, Ericscript (v0.5.5) and rMATS (v3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively. Expression level of gene was calculated by RSEM (v1.2.8). The differential expression analysis was performed using the DESeq2 (v1.16.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read and FPKM

source_name: Cortex

extract_protocol:
Total RNA was extracted using an RNeasy Micro Kit (QIAGEN)
The quality of RNA samples was assessed using an RNA 6000 Pico Kit (Agilent, Santa Clara, CA, USA) and 2100 Bioanalyzer (Agilent). 1 µg of total RNA was used for the construction of sequencing libraries. The sequencing libraries for RNA-seq were prepared using Hieff NGS™ Ultima Dual-mode mRNA Library Prep Kit according to manufacturer’s protocol, and were sequenced with DNBSEQ-G400 (MGI) based on PE150 strategy.

treatment_protocol: Lipopolysaccharide (LPS; Escherichia coli 055:B5) were intraperitoneally injected into mice at a dose of 500 µg/kg body weight once per day for four consecutive days. For control, the same amount of normal saline (0.1 mL for each 10 g body weight) was injected once per day for four consecutive days.

value: Cortex

value: Microglia

value: LPS


title: N2control_for ceELAC2_RIP_mito

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

data_processing:
For mecciRNA identification, the clean data were filtered by bowtie2 (v 1.2.1) to remove reads mapped to rDNA. The left reads were mapped to the reference genome by bwa-men (v 0.7.17). The discontinuously mapped reads were extracted and mapped again to mitochondrial genome by bowtie (v 1.2.1). mecciRNA candidates were predicted by pepline mentioned in our article.
For ng-circRNA identification, the clean reads not aligned to rDNA sequences filtered by bowtie2 were mapped to the reference genome by bwa-mem. circRNA candidates were predicted by CIRI2 (v 2.0.6).
For smallRNA-seq analysis, the raw data were trimmed by cutadapt (v 1.15) to remove adaptor sequences to get clean data. The clean data were mapped to the mitochondrial genome with bowtie, and the forward or reverse mapping reads were extracted by samtools (v 1.10). The distribution of peaks was generated with an integrative genomics viewer (IGV) (v 2.11.0).
Assembly: hg38, mm10, ce11
Supplementary files format and content: comma-separated value files include count values for each Sample
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: bigwig

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
The isolated mitochondria, total cells were lysed in TRizol reagent (Life Technologies). RNA from  mitochondia, whole cell, mitochondrial fractions and RNA-IP were extracted by using TRizol reagent according to the manufacturer’s instructions.
For small RNA seq, the small RNA bands in fractions 2–4 and the input were excised from the gel and RNAs were purified. Small RNA libraries were constructed with NEBNext Multiplex Small RNA Library Prep Set for Illumina following the manufacturer’s protocol. For total RNA and mitochondrial RNA sequencing, rRNA is removed from the total RNA sample using TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599), and sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) following the manufacturer’s recommendations. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.
For TRAP1 RIP and ATP5B RIP, sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) following the manufacturer’s recommendations.
For other RIP-seq, NEB Next Ultra RNA Library Prep Kit (NEB) was used for library construction of immunoprecipitated RNA. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.

value: whole worm

value: WT

tag: library type

value: RIP-seq


title: WholeCell_replicate1_no-stress_Nab2-IDRmutant

value: no stress


title: pooled cardiac TAC WT endothelial cells

value: mixed background


title: 02_EC2_OE

data_processing:
The reads were mapped to the reference genome mm10 (version 3.0.0) using CellRanger Default settings . Analysis was conducted using the Seurat package (version 4.0.2) in R (version 4.0.5).
Data were filtered for cells expressing at least 200 genes and less than 25% mitochondrial counts before the matrix was log-normalized and scaled
Genome_build: mm10
Supplementary_files_format_and_content: txt output from filter_barcode were used

growth_protocol: hprt-Sox9fl/fl mice were crossed with Cdh5-Cre+/- and interbred homozygous for Sox9fl/fl and hemizygous for Cre

treatment_protocol: Mice were injected with 0.5 mg Tamoxifen for 5 consecutive days 1 M prior to organ harvest

value: heart

value: Sox9 overexpression


title: Blastocyst (day 0)

description: 10x Genomics

value: Embryonic and extra-embryonic cells

value: Embryo


title: CD11b+ cells, LPS4x_2


title: CD11b+ cells, Control_3

value: Normal saline


title: WholeCell_replicate1_stress_Nab2-wild type

value: stress

value: MAT alpha his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 NAB2::NAB2-yEGFP-HISMX


title: WholeCell_replicate1_no-stress_Nab2-wild type


title: 01_EC1_WT

value: ctrl


title: N2control_for ceSUPV3L1_RIP_mito

institute: University of Science and Technology of China


title: ceSUPV3L1_RIP_mito


title: MCPs-EVs

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

country: South Korea

institute: Inha university hospital

description: Mouse-PC-purified-EV

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mmu (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: mmu
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: mouse corpus cavernous pericyte cultured medium

growth_protocol: The primary MCPs were prepared from mouse penis tissue as previously described.17,29 The cultured complement DMEM (Gibco, Carlsbad, CA, USA)containing 20% fetal bovine serum (FBS, Gibco), 1% penicillin/streptomycin (Gibco), and 10 nM human pigment epithelium-derived factor (PEDF, Sigma-Aldrich, St Louis, MO, USA). We changed the medium every 2 days, and after 10 days the cells were sub-cultured. Cells from passages 2 to 4 were used for all experiments.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small  RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

treatment_protocol: MCPs-derived EVs (MCPs-EVs) were isolated from MCPs cultured medium by using a Commercials EV isolation kit (ExoQuick-TC, System Biosciences, LLC., Palo Alto, CA, USA) following manufacturers’ instructions.

value: mouse cavernous pericyte


title: CD11b+ cells, Control_1

value: Cortex


title: CD11b+ cells, Control_2

value: Microglia


title: PBAT sample for MEF, replicate 2

value: embryo

value: mouse embryonic fibroblast (MEF)

value: wild type

value: 2D culture in MEF medium

value: E13.5 embryos


title: BDP3_HA 7

status: Public on Dec 18 2023

city: Indianapolis

first: Victoria

last: Jeffers

state: IN

address: Pharmacology & Toxicology

institute: Indiana University School of Medicine

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic (version 0.33) with these parameters: ILLUMINACLIP:<adapters.fasta>:3:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:40
Trimmed reads were mapped on the Toxoplasma gondii GT1 using Bowtie2 version 2.3.4.2 with default parameters
MACS2 version 2-1.2_dev was used to callpeaks with the following parameters non-standard parameters: -f BEDPE -g 65000000 --buffer-size 100000000
Genome_build: genome-name: Toxoplasma gondii GT1; build-accession: GCA_000149715.2; genome-version:TGGT1; genome-build: European Nucleotide Archive TGGT1; last-updated: 2013-07

organism: Toxoplasma gondii

source_name: Tachyzoite

growth_protocol: Tachyzoites were inoculated onto confluent monolayers of primary human foreskin fibroblasts to invade and replicate for 32 hours when parasitophorus vacuoles contained 16-32 parasites

extract_protocol:
Parasites were isolated from infected host cells by syringe-lysis, then nuclear lysates enriched by cellular fractionation were sonicated and clarified by centrifugation. Protein-DNA complexes were immunoprecipitated with antibody-coupled magnetic beads.
1 µg ChIP DNA were used in library preparation using NEBNext Ultra II DNA library prep kit for Illumina (NEB cat#E7645) and the protocol from the manufacturer was followed. A unique 8nt barcode was added to each sample for multiplex sequencing.

treatment_protocol: Normal growth conditions

value: Tachyzoite

tag: genotype/variation

value: RH delta HX deltaKu80 BDP3_3xHA

tag: chip antibody

value: Anti-HA coupled to magnetic beads (ThermoFisher # 88836)


title: BDP3_HA 8


title: Parental 2

value: RH deltaHX deltaKu80


title: Parental 1


title: sgFXN_Rep2

city: Rehovot

first: Tslil

last: Ast

address: 234 Herzl St.

country: Israel

institute: The Weizmann Institute of Science

data_processing:
Analysis of genetic interactors was performed as previously described (PMID: 31730859). Briefly, raw sgRNA read counts were normalized to reads per million and then log2 transformed using the following formula:
Log2(Reads from an individual sgRNA/Total reads in the sample x E6 + 1)
Log2 fold-change of each sgRNA was determined relative to guide abundance in the lentiviral library. The replicates were paired throughout the course of the screens.
For each gene and for each replicate, the mean log2 fold-change in the abundance of all 4 sgRNAs was calculated. Log2 fold-changes were averaged by taking the mean across replicates. For each treatment, a null distribution was defined by the 3,726 genes with lowest expression (log2 FPKM = −7) according to publicly available K562 RNA-seq dataset (sample GSM854403 in GEO series GSE34740). To score each gene, its mean log2 fold-change across replicates was Z-score transformed, using the statistics of the null distribution.
Assembly: hg19
Supplementary files format and content: Txt file: counts per guide
Library strategy: gDNA sequencing

growth_protocol: Cells were maintained in DMEM (GIBCO) with 25 mM glucose, 10% fetal bovine serum (FBS, Invitrogen), 4mM Glutamine, 1 mM sodium pyruvate, 50 µg/mL uridine, and 100 U/mL penicillin/ streptomycin under 5% CO2 at 37°C

extract_protocol:
Genomic DNA was isolated using the XL Maxi NucleoSpin Blood kit (Macherey-Nagel) according to the manufacturer’s protocol
sgRNA sequences were amplified from gDNA by PCR using Ex Taq DNA polymerase (TaKaRa). For each reaction, a maximum of 10 µg gDNA was used with primers containing barcodes and Illumina sequencing reactions, and amplified with 28 PCR cycles.


title: sgControl_Rep2


title: CD11b+ cells, LPS4x_1

tag: treatment

value: LPS


title: PBAT sample for MEF, replicate 1

tag: cell type


title: sgControl_Rep1


title: ceELAC2_RIP_mito

value: whole worm

value: RIP-seq


title: sgFXN_Rep1


title: Parental 3


title: Beta vaccinated replicate3

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Sequencing adapters were trimmed from reads using Cutadapt.
Trimmed reads were pseudoaligned to the golden hamster transcriptome with Kallisto.
Estimated gene counts were obtained by combining transcript-level counts using tximport.
Assembly: MesAur1.0
Supplementary files format and content: count_matrix.txt: tab-separated estimated read counts per gene
Supplementary files format and content: tpm_matrix.txt: tab-separated transcripts per million (TPM) per gene

organism: Mesocricetus auratus

source_name: right lung caudal lobe

extract_protocol:
Right lung caudal lobe was harvested from the animals and homogenized in trizol. RNA purification was performed with the kit RiboPure™ RNA Purification Kit following manufacturer’s instructions.
Sequencing libraries were generated with the Illumina Total RNA Prep with Ribo-Zero Plus kit.

value: right lung caudal lobe

tag: vaccination

value: Pfizer BNT162b2

tag: viral challenge

value: Beta


title: Beta vaccinated replicate1


title: Beta vaccinated replicate2


title: Beta vaccinated replicate4


title: Beta unvaccinated replicate5

value: PBS control


title: Alpha unvaccinated replicate2

value: Alpha


title: Beta vaccinated replicate5


title: Alpha unvaccinated replicate3


title: Alpha vaccinated replicate3


title: Alpha unvaccinated replicate1


title: Alpha unvaccinated replicate4


title: Alpha vaccinated replicate5


title: Alpha unvaccinated replicate5


title: Alpha vaccinated replicate4


title: Alpha vaccinated replicate1


title: Alpha vaccinated replicate2


title: Beta unvaccinated replicate4


title: Beta unvaccinated replicate3


title: Beta unvaccinated replicate1


title: Beta unvaccinated replicate2


title: Mu vaccinated replicate5

value: Mu


title: Mu vaccinated replicate4


title: Mu unvaccinated replicate3


title: Mu unvaccinated replicate2


title: Mu unvaccinated replicate1


title: Delta vaccinated replicate3

value: Delta


title: Delta vaccinated replicate5


title: Mu vaccinated replicate3


title: Mu vaccinated replicate1


title: Mu unvaccinated replicate4


title: Delta vaccinated replicate1


title: Delta unvaccinated replicate5


title: Mu vaccinated replicate2


title: Delta vaccinated replicate2


title: Delta unvaccinated replicate3


title: Delta vaccinated replicate4


title: Delta unvaccinated replicate4


title: Delta unvaccinated replicate2


title: Delta unvaccinated replicate1


title: WA1/2020 vaccinated replicate5


title: Mu unvaccinated replicate5


title: WA1/2020 vaccinated replicate2


title: WA1/2020 vaccinated replicate4


title: WA1/2020 vaccinated replicate3


title: WA1/2020 vaccinated replicate1


title: WA1/2020 unvaccinated replicate5


title: WA1/2020 unvaccinated replicate4


title: WA1/2020 unvaccinated replicate3


title: WA1/2020 unvaccinated replicate2


title: Mock vaccinated replicate5

value: Mock


title: Mock vaccinated replicate4


title: Mock vaccinated replicate3


title: Mock unvaccinated replicate3


title: Mock unvaccinated replicate2


title: Mock unvaccinated replicate1


title: WA1/2020 unvaccinated replicate1


title: HA-INO-CAR-T cells, donor 13

city: Stanford

first: Yiyun

address: 265 Campus Dr Room G2105

department: Stanford Cancer Institute

institute: Stanford University

description:
DN13_ino
TPM_HA_ino_glucose.csv

data_processing:
Reads mapping and counting were performed using STAR (version 2.7.6a) with GRCh38 as reference genome, HTSeq-count tools respectively.
Assembly: hg38
Supplementary files format and content: Data transcripts per million summarized to gene level. Each column in the table is a sample. Each row is a gene.

source_name: CAR T cells

extract_protocol:
Total mRNA was isolated using Qiagen RNEasy Plus mini-isolation kit.
Libraries and RNA-seq were performed by Novogene (Sacramento, CA) and 150 bp paired-end sequencing at a depth of 3×107 reads per sample was obtained using the Illumina NovaSeq6000 platform.

value: CAR T cells

value: Inosine


title: HA-INO-CAR-T cells, donor 11

description:
DN11_ino
TPM_HA_ino_glucose.csv


title: HA-CAR-T cells, donor 13

description:
DN13_glucose
TPM_HA_ino_glucose.csv

value: Glucose


title: HA-INO-CAR-T cells, donor 12

description:
DN12_ino
TPM_HA_ino_glucose.csv


title: Mock unvaccinated replicate4


title: HA-CAR-T cells, donor 12

description:
DN12_glucose
TPM_HA_ino_glucose.csv


title: Mock vaccinated replicate2


title: genomic DNA from septic shock patient 4

type: genomic

city: València

first: José Luis

last: García-Giménez

state: València

address: Avenida Blasco Ibáñez, 15

department: Departamento de Fisiología. Facultad de Medicina y Odontología

institute: Universitat de València

description: genomic DNA from septic shock patient 4

hyb_protocol: The bisulphite treatment of DNA was followed by a whole genome amplification step, enzymatic endpoint fragmentation, precipitation and resuspension, and finally, the hybridization to Illumina Infinium MethylationEPIC BeadChip  v1.0 using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina HiScan SQ scanner

data_processing: House-made R scripts

label: biotin and DNP

label_protocol: The nucleotides incorporated for the single base extension were labeled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP)

extract_protocol: DNA was purified from leukocytes of patients’ whole blood collected in anti-coagulant (EDTA K2) tubes. All samples were collected within the first 24 hours of ICU admission. DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen Inc., Germantown, MD USA).

value: leukocytes

tag: disease

value: Septic shock


title: genomic DNA from septic shock patient 2

description: genomic DNA from septic shock patient 2


title: CD39-KO HA-CAR-T cells, donor 504

description:
D504-CD39KO
TPM_KO_OE.csv


title: ADA-OE HA-CAR-T cells, donor 43

description:
D43-ADA
TPM_KO_OE.csv

value: ADA-OE


title: Mock vaccinated replicate1


title: control HA-CAR-T cells, donor 43

description:
D43-AAVS1
TPM_KO_OE.csv


title: A2aR-KO HA-CAR-T cells, donor 43

description:
D43-A2aRKO
TPM_KO_OE.csv


title: CD73-KO HA-CAR-T cells, donor 504

description:
D504-CD73KO
TPM_KO_OE.csv


title: CD73-KO HA-CAR-T cells, donor 48

description:
D48-CD73KO
TPM_KO_OE.csv


title: ADA-OE HA-CAR-T cells, donor 504

description:
D504-ADA
TPM_KO_OE.csv


title: genomic DNA from critically ill patient 3

value: CIP


title: genomic DNA from sepsis patient 2

description: genomic DNA from sepsis patient 2

value: Sepsis


title: genomic DNA from critically ill patient 1


title: genomic DNA from critically ill patient 4


title: genomic DNA from sepsis patient 1

description: genomic DNA from sepsis patient 1


title: HA-CAR-T cells, donor 1

description:
DN4 HA
Glucose_HA_CAR_T.bw
ATAC_peak.bed
ATAC_peak_annotation.csv

data_processing:
The ENCODE ATAC-seq pipeline v2.0.3 was used for quality control and processing of ATAC-seq using default parameters. Briefly, raw ATAC-seq reads were trimmed with cutadapt to remove Illumina Nextera adapter sequences and aligned to hg19 using Bowtie2. Uniquely aligned reads were identified using picard MarkDuplicates with 73–85% non-duplicates mapped reads among all the samples. Peak from individual samples was called on Tn5-corrected insertion sites using MACS2. Reads from mitochondria and reads of low mapping quality (MAPQ<30) were excluded. A union peak set was compiled by extending peak summits to 500 bp, merging all summits, running bedtools cluster, selecting summits with the highest MACS2 score. Peaks intersecting with ENCODE hg19 blacklisted regions or regions on chrY and chrX were removed.
Assembly: hg19
Supplementary files format and content: bigwig genome wide signal track, ATAC peaks and annotations

extract_protocol:
Approximately 100,000 CAR T cells were used per sample. Nuclei were isolated with ATAC-LB (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL) and used for tagmenta- tion using Nextera DNA Library Preparation Kit (Illumina) from three donors.
After tag- mentation DNA was purified with MinElute PCR Purification Kit (Qiagen). Tagmented DNA was then amplified with Phusion high-fidelity PCR master mix (NEB) using 14 PCR cycles. Amplified libraries were purified again with MinElute PCR Purification Kit. Fragment distribution of libraries was assessed with Agilent Bioanalyzer and libraries were sequenced on the Illumina NovaSeq 6000 PE150 platform at a depth of 3 × 107 reads per sample. Sequencing was performed by Novogene (Sacramento, CA)


title: control HA-CAR-T cells, donor 504

description:
D504-AAVS1
TPM_KO_OE.csv


title: genomic DNA from septic shock patient 1

description: genomic DNA from septic shock patient 1


title: CD39-KO HA-CAR-T cells, donor 48

description:
D48-CD39KO
TPM_KO_OE.csv


title: ADA-OE HA-CAR-T cells, donor 48

description:
D48-ADA
TPM_KO_OE.csv


title: A2aR-KO HA-CAR-T cells, donor 48

description:
D48-A2aRKO
TPM_KO_OE.csv


title: A2aR-KO HA-CAR-T cells, donor 504

description:
D504-A2aRKO
TPM_KO_OE.csv


title: HA-INO-CAR-T cells, donor 1

description:
DN4 HA INO
Inosine_HA_CAR_T.bw
ATAC_peak.bed
ATAC_peak_annotation.csv


title: CD73-KO HA-CAR-T cells, donor 43

description:
D43-CD73KO
TPM_KO_OE.csv


title: CD39-KO HA-CAR-T cells, donor 43

description:
D43-CD39KO
TPM_KO_OE.csv


title: HA-INO-CAR-T cells, donor 3

description:
DN3 HA INO
Inosine_HA_CAR_T.bw
ATAC_peak.bed
ATAC_peak_annotation.csv


title: genomic DNA from sepsis patient 3

description: genomic DNA from sepsis patient 3


title: HCC38 HLA HI Rep 2

city: San Francisco

first: Sourav

last: Bandyopadhyay

address: 1450 3rd Street

department: Helen Diller Family Comprehensive Cancer Center

institute: University of California, San Francisco

data_processing:
HISAT2 v2.0.5
Sequencing analysis was performed by Novogene.
Differential gene expression analysis utilizing DESeq2 v1.20.0 was performed and provided by Novogene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw couts, FKPM values, and normalized values for each grouped sample.

growth_protocol: Breast cancer cell lines were grown according to published guidelines except for SKBR3 cells which were cultured using RPMI media supplemented with 10% fetal bovine serum (FBS) and 1% pen/strep. All cell lines tested negative for mycoplasma contamination.

extract_protocol:
Total RNA was extracted using RNAeasy mini kit (Qiagen). 400ng of total RNA was provided to Novogene.
A complementary DNA library was prepared and Illumina RNAseq performed by Novogene (https://www.novogene.com/us-en/).

treatment_protocol: Cancer cells were flow sorted on a Sony SH800S Cell Sorter (Sony) using anti-human HLA-A/B/C conjugated to Alexa Fluor 488 (560169, BD Pharmingen) at the manufacturer’s recommended concentration. Gating of positive and negative cells was defined by the unstained control, and cells were sorted into representative high and low expressing populations as indicated. All sorting was performed to separate a high and low fraction constituting the top 5% and bottom 10% of cells.

tag: group

value: HLA HI


title: genomic DNA from septic shock patient 5

description: genomic DNA from septic shock patient 5


title: HCC38 HLA HI Rep 1


title: HCC38 HLA LO Rep 1

value: HLA LO


title: control HA-CAR-T cells, donor 48

description:
D48-AAVS1
TPM_KO_OE.csv


title: HA-INO-CAR-T cells, donor 2

description:
DN2 HA INO
Inosine_HA_CAR_T.bw
ATAC_peak.bed
ATAC_peak_annotation.csv


title: MDA-MB-468 HLA LO Rep 2


title: MDA-MB-468 HLA LO Rep 1


title: HCC38 HLA LO Rep 2


title: MDA-MB-468 HLA HI Rep 2


title: genomic DNA from critically ill patient 2


title: genomic DNA from septic shock patient 3

description: genomic DNA from septic shock patient 3


title: HCT116 cells, 1ug/mL LPS for 24h

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Raw sequence reads were trimmed for adaptor sequence/low quality sequence using cutadapt (v1.9), FQ_clean_v2.0.pl, and Trimmomatic (v0.39)
Trimmed sequence reads were mapped to hg38 using HISAT2 (v2.1.0) (parameters: -p 8 --dta -x hg38_tran)
Read count extraction was performed using featureCounts (v2.0.1) (parameters: -T 6 -p)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: HT29 and HCT116 cell lines were cultured in Advanced DMEM/F-12 medium (Gibco, USA), supplemented with 10% fetal bovine serum (Sigma, USA), 1% GlutaMAX Supplement (Gibco, USA), and 1% TransSafe Mycoplasma Prevention Reagent (TRANS, China). The culture conditions were maintained at 37 °C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Ger-many).
RNA libraries for RNA-seq were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s instructions.

treatment_protocol: To establish an in vitro inflammatory model of intestinal epithelial cells, the cells were treated with lipopolysaccharide (LPS, 1 ug/mL) (Sigma‒Aldrich, USA) for a duration of 24 h.

value: 1ug/mL LPS for 24h


title: MDA-MB-468 HLA HI Rep 1


title: HCT116 cells, control

value: control


title: HA-CAR-T cells, donor 3

description:
DN3 HA
Glucose_HA_CAR_T.bw
ATAC_peak.bed
ATAC_peak_annotation.csv


title: HT29 cells, 1ug/mL LPS for 24h


title: HT29 cells, control


title: HA-CAR-T cells, donor 2

description:
DN2 HA
Glucose_HA_CAR_T.bw
ATAC_peak.bed
ATAC_peak_annotation.csv


title: RPE1_cells

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

institute: EPFL

data_processing:
Raw fastq files were processed with CellRanger using the default human reference transcriptome to obtain count matrices. To obtain unspliced and spliced count matrices, we used velocyto version 0.17.17.
Assembly: GRCh38
Supplementary files format and content: Processed data files include the CellRanger output filtered_bc_matrix folders as well as a loom file corresponding to the output from running velocyto version 0.17.17 with default parameters.

molecule: cytoplasmic RNA

extract_protocol:
FUCCI-RPE-1 cells (see Fig. 4), a gift from Battich et al64, were cultured at 37°C and 5% CO2 in DMEM/F12 medium (Gibco 11320033) supplemented with 1% NEAA (Gibco 11140-035), 1% Penicillin/Streptomycin (Sigma Aldrich G6784) and 10% FBS (Gibco 10437-028). Additional RPE-1 cells (see Fig. 5) were obtained from ATCC and cultured at 37°C, 20% O2, and 5% CO2 in DMEM/F12 medium (Gibco 21331-020) supplemented with 1% MEM NEAA (Sartorius 01-340-1B), 0.5% sodium pyruvate 1% penicillin/streptomycin/glutamine, and 10% FBS. Media was replaced daily and cells were passaged twice a week. RPE-1 cells were maintained in culture for at least two passages and confirmed to be free of mycoplasma.
For the preparation of scRNA-seq libraries, an experimental setup was designed to mimic the conditions used for live-cell imaging. FUCCI-RPE-1 cells were seeded (7000 cells/cm²) in duplicate 2 days before collection.  On collection day, cells were detached with trypsin, washed with PBS, counted and diluted to a cell concentration of 1000 cells/uL. Barcoded cDNA libraries were generated from single cell suspensions using the 10x Genomics Chromium v3.1 dual-index system. The procedure was done in accordance with the manufacturer's instructions, with a goal of 4,000 cells per library. Samples were individually indexed and evenly pooled together. After quality control, libraries were sequenced on an Illumina HiSeq4000 platform, with a depth of approximately 300 million reads per sample, by the EPFL Gene Expression Core Facility (GECF). Similarly, RPE-1 cells were detached using Trypsin–EDTA solution A 0.25% (Biological Industries; 030501B) for 5 min at 37°C. Trypsin was neutralized with medium including 10% FBS and cells were centrifuged at 250 rcf for 5 min, followed by washing and resuspension in PBS with 0.04% BSA. The cell suspension was filtered with a 40-μm cell strainer to remove cell clumps. A cell viability percentage higher than 90% was determined by trypan blue staining. Cells were diluted to a final concentration of 700 cells per μl. scRNA-seq libraries were generated using the 10x Genomics Chromium v3.1 dual-index system. The procedure was done in accordance with the manufacturer's instructions, with a goal of 3,000 cells per library. Samples were then indexed and sequenced on an Illumina NovaSeq 6000 platform by the EPFL Gene Expression Core Facility (GECF).


title: gD/NA,NC,rep2

city: South San Francisco

first: Daniel

last: Le

address: 1 DNA Way

institute: Genentech

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor
reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed
reads were aligned to the human reference genome (human: GRCh38.p10) using GSNAP version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap’)
Transcript annotation was based on the Gencode genes data base (human: GENCODE 27). To quantify gene expression levels, the number of reads mapping unambiguously to the exons of each gene was calculated
Assembly: GRCh38.p10
Supplementary files format and content: Comma-separated text file of raw counts for each sample

source_name: blood

extract_protocol:
Cells were pelleted and RNA was extracted using an RNeasy mini kit (Qiagen, cat#74014)
Truseq Stranded mRNA kit (Illumina) was used with an input of 100ng of total RNA

treatment_protocol: Each well was treated in triplicate with 100nM of the indicated mimetic antibody format or recombinant IL-2 and incubated at 37°C and 5% CO2 for 24 hours

value: blood

value: primary

value: CD8+ T cells

value: WT

value: gD/NA,NC


title: gD/NA,NC,rep1


title: IL2/NA,PC,rep2


title: gD/NA,NC,rep3


title: IL2/NA,PC,rep3


title: B09/G28,contorsbody,rep3


title: B09/G28,IgG,rep1


title: B09/G28,IgG,rep2


title: B09/G28,contorsbody,rep1


title: B09/G02,contorsbody,rep2


title: B09/G02,contorsbody,rep3


title: B09/G28,IgG,rep3


title: B09/G02,contorsbody,rep1


title: B09/G02,IgG,rep1


title: B09/G02,IgG,rep3


title: B10/G28,iAb,rep3


title: B09/G02,IgG,rep2


title: B10/G28,iAb,rep1


title: B10/G28,IgG,rep2


title: B10/G28,iAb,rep2


title: B10/G25,iAb,rep2


title: B10/G28,IgG,rep3


title: IL2/NA,PC,rep1


title: B10/G28,IgG,rep1


title: B10/G25,iAb,rep1


title: B10/G25,IgG,rep3


title: B09/G28,contorsbody,rep2


title: B10/G25,IgG,rep2


title: HA-CAR-T cells, donor 11

last: Chen

description:
DN11_glucose
TPM_HA_ino_glucose.csv

value: CAR T cells


title: #8-13-15 ADT/HTO

city: Suita

first: Xiuyuan

last: Lu

state: Osaka

address: 3-1 Yamadaoka

department: IFReC

institute: Osaka University

description: 10x Genomics

library_source: other

data_processing:
The raw reads were processed by Cell Ranger 6.0.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5 (RNA and feture barcodes)
Supplementary files format and content: CellRanger output files: filtered_contig_annotations.csv (TCR)

molecule: protein

source_name: PBMC

extract_protocol:
On day 10 of the culture, cells were washed and stained with anti-human CD3 and TotalSeq-C antibodies (see ADT/HTO_ information.csv). Proliferated T cells (CD3+CTVlow) were sorted and used for single-cell TCR and RNA sequencing analyses.
Single cell library was prepared using the reagents from 10x Genomics following the manufacturer’s instructions. After reverse transcription, cDNA was amplified for 14 cycles, and up to 50 ng of cDNA was used for construction of gene expression and TCR libraries. Libraries were sequenced in paired-end mode.

treatment_protocol: PBMCs were labeled with CellTrace Violet (CTV) and cultured in the presence of SARS-CoV-2 S peptide pool (15-mer, with 11-mer overlap) that covers whole S protein of Wuhan strain, mutations in S proteins of Delta, Omicron BA.1 and BA.2 strains. Human recombinant IL-2 (1ng/ml), IL-7 (5ng/ml) and IL-15 (5ng/ml) were supplemented on day 2, day 5 and day 8 of the culture.

value: PBMC

value: T cell

value: Mixed sample (3wks, 6wks, 24wks from donor #8,#13,#15)


title: #8-13-15 RNA

description: 10x Genomics


title: pre RNA

description: 10x Genomics


title: pre TCR

description: 10x Genomics


title: #25-28 ADT/HTO

description: 10x Genomics

value: Mixed sample (3wks, 6wks, 24wks from donor #25,#28)


title: #25-28 RNA

description: 10x Genomics


title: pre ADT/HTO

description: 10x Genomics


title: #4-17 RNA

description: 10x Genomics

value: Mixed sample (3wks, 6wks, 24wks from donor #4,#17)


title: #4-17 TCR

description: 10x Genomics


title: Mock unvaccinated replicate5

value: right lung caudal lobe

value: PBS control

value: Mock


title: B10/G25,iAb,rep3


title: #27 TCR

description: 10x Genomics

value: Mixed sample (3wks, 6wks, 24wks)


title: #27 ADT/HTO

description: 10x Genomics


title: #8-13-15 TCR

description: 10x Genomics


title: Pt 23 - treatment-naïve biopsy

city: Baltimore

first: Roy

last: Elias

state: Maryland

address: 201 N Broadway

institute: Johns Hopkins University

description:
S18_44973Bx_rsem_hg38.genes.results
expected_count.txt column name:  S18_44973Bx_rsem_hg38.genes.results

data_processing:
Illumina's CASAVA 1.8.4 was used to convert BCL files to FASTQ files. Default parameters were used.
rimgalore v0.6.3 was used to trim the reads. Default parameters were used.
rsem-1.3.0 was used for running the alignments as well as generating gene and transcript expression levels. The ‘rsem-calculate-expression’ module was used with the following options: --star --star-gzipped-read-file --calc-ci --star-output-genome-bam --paired-end --forward-prob 0
Assembly: hg38
Supplementary files format and content: tab delimited text file contains expected counts for each sample

source_name: treatment-naïve biopsy

extract_protocol:
Six image-guided percutaneous biopsy cores of primary tumors were acquired prior to starting nivolumab for each patient.  One core was sent for standard-of-care histological analysis for clinical diagnosis, while the other 5 cores were retained for research, including 2 cores that were placed in RNAlater for downstream RNA extraction and 3 cores that were paraffin-embedded.
Following treatment with nivolumab, 3 non-necrotic pieces of tumor from the nephrectomy specimen, each measuring 1 x 1 x 0.5 cm, were harvested for research use, including one piece that was paraffin-embedded, one freshly processed for lymphocyte isolation, and one placed in RNAlater for downstream RNA extraction. Formalin-fixed, paraffin-embedded (FFPE) slides were freshly cut and stored at -20C until nucleic acid extraction was performed. Samples were processed in accordance with the AllPrep DNA/RNA FFPE kit (Qiagen, Cat# 80234). Briefly, samples undergo a quick lysis, followed by a cooling step and centrifugation to release and collect RNA. Additional steps are taken to reverse crosslinking and facilitate binding to RNA purification columns. An on-column DNase step was performed on the RNA purification column, to remove any contaminating DNA. After wash steps, RNA was eluted from the columns.  Nucleic acid yield and quality were first assessed using a NanoDrop ND-1000 spectrophotometer and later by quantifying the abundance of ribosomal RNA fractions with Experion (Bio-Rad) and/or Agilent 2100 Bioanalyzer.
Illumina TruSeq RNA Exome

treatment_protocol: systemic nivolumab 3mg/kg weekly x3 weeks -- includes paired (matched) treatment-naïve biopsy tissue and treatment-exposed nephrectomy tissue

tag: disease state

value: non-metastatic ccRCC

tag: individual

value: Pt 23

value: treatment-naïve biopsy


title: Pt 20 - post-treatment nephrectomy

description:
S18_30705NxT_2H_rsem_hg38.genes.results
expected_count.txt column name:  S18_30705NxT_2H_rsem_hg38.genes.results

source_name: post-treatment nephrectomy

value: Pt 20

value: post-treatment nephrectomy


title: #27 RNA

description: 10x Genomics


title: Pt 22 - post-treatment nephrectomy

description:
S18_38659NxT_1L_rsem_hg38.genes.results
expected_count.txt column name:  S18_38659NxT_1L_rsem_hg38.genes.results

value: Pt 22


title: Pt 20 - treatment naïve biopsy

description:
S18_18563Bx_rsem_hg38.genes.results
expected_count.txt column name:  S18_18563Bx_rsem_hg38.genes.results


title: Pt 21 - post-treatment nephrectomy

description:
S18_33695NxT_1K_rsem_hg38.genes.results
expected_count.txt column name:  S18_33695NxT_1K_rsem_hg38.genes.results

value: Pt 21


title: Pt 19 - post-treatment nephectomy

description:
S18_22484NxT_1D_rsem_hg38.genes.results
expected_count.txt column name:  S18_22484NxT_1D_rsem_hg38.genes.results

value: Pt 19


title: Pt 22 - treatment-naïve biopsy

description:
S18_23078Bx_rsem_hg38.genes.results
expected_count.txt column name:  S18_23078Bx_rsem_hg38.genes.results


title: B10/G25,IgG,rep1

value: blood

tag: cell line

value: primary

value: CD8+ T cells

value: WT


title: Pt 21 - treatment-naïve biopsy

description:
S18_17753Bx_rsem_hg38.genes.results
expected_count.txt column name:  S18_17753Bx_rsem_hg38.genes.results

tag: tissue


title: Pt 15 - treatment-naïve biopsy

description:
S17_53462Bx_rsem_hg38.genes.results
expected_count.txt column name:  S17_53462Bx_rsem_hg38.genes.results

value: Pt 15


title: Pt 12 - post-treatment nephrectomy

description:
S17_49942NxT_1I_rsem_hg38.genes.results
expected_count.txt column name:  S17_49942NxT_1I_rsem_hg38.genes.results

value: Pt 12


title: Pt 15 - post-treatment nephrectomy

description:
S17_66030NxT_1C_rsem_hg38.genes.results
expected_count.txt column name:  S17_66030NxT_1C_rsem_hg38.genes.results


title: #4-17 ADT/HTO

description: 10x Genomics

value: PBMC

value: T cell

value: Mixed sample (3wks, 6wks, 24wks from donor #4,#17)


title: #25-28 TCR

description: 10x Genomics

value: Mixed sample (3wks, 6wks, 24wks from donor #25,#28)


title: Pt 14 - treatment-naïve biopsy

description:
S17_41037Bx_rsem_hg38.genes.results
expected_count.txt column name:  S17_41037Bx_rsem_hg38.genes.results

value: non-metastatic ccRCC

value: Pt 14


title: Pt 8 - post-treatment nephrectomy

description:
S16_59199NxT_1C_rsem_hg38.genes.results
expected_count.txt column name:  S16_59199NxT_1C_rsem_hg38.genes.results

value: Pt 8


title: Pt 11 - post-treatment nephrectomy

description:
J15179_11NxT_rsem_hg38.genes.results
expected_count.txt column name:  J15179_11NxT_rsem_hg38.genes.results

value: Pt 11

value: post-treatment nephrectomy


title: Pt 1 - post-treatment nephrectomy

description:
S16_36657NxT_1B_rsem_hg38.genes.results
expected_count.txt column name:  S16_36657NxT_1B_rsem_hg38.genes.results

value: Pt 1


title: Pt 5 - post-treatment nephrectomy

description:
S16_57620NxT_1F_rsem_hg38.genes.results
expected_count.txt column name:  S16_57620NxT_1F_rsem_hg38.genes.results

value: Pt 5


title: Pt 14 - post-treatment nephrectomy

description:
J15179_14NxT_rsem_hg38.genes.results
expected_count.txt column name:  J15179_14NxT_rsem_hg38.genes.results


title: Pt 4 - treatment-naïve biopsy

description:
J15179_18Bx_rsem_hg38.genes.results
expected_count.txt column name:  J15179_18Bx_rsem_hg38.genes.results

value: Pt 4

value: treatment-naïve biopsy


title: Pt 3 - post-treatment nephrectomy

description:
S16_55930NxT_1F_rsem_hg38.genes.results
expected_count.txt column name:  S16_55930NxT_1F_rsem_hg38.genes.results

value: Pt 3


title: Pt 10 - treatment-naïve biopsy

description:
J15179_10Bx_rsem_hg38.genes.results
expected_count.txt column name:  J15179_10Bx_rsem_hg38.genes.results

value: Pt 10


title: Pt 8 - treatment-naïve biopsy

description:
J15179_08Bx_rsem_hg38.genes.results
expected_count.txt column name:  J15179_08Bx_rsem_hg38.genes.results


title: Pt 9 - post-treatment nephrectmy

description:
J15179_09NxT_rsem_hg38.genes.results
expected_count.txt column name:  J15179_09NxT_rsem_hg38.genes.results

value: Pt 9


title: Pt 3 - treatment-naïve biopsy

description:
J15179_03Bx_rsem_hg38.genes.results
expected_count.txt column name:  J15179_03Bx_rsem_hg38.genes.results


title: Pt 4 - post-treatment nephrectomy

description:
J15179_04NxT_rsem_hg38.genes.results
expected_count.txt column name:  J15179_04NxT_rsem_hg38.genes.results


title: PaxWholeBlood, pre-BAL[96196P]

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

institute: University of Washington

data_processing:
Pooled libraries were sequenced on a NovaSeq 6000 S1 flowcell with RTA v3.4.4 and demultiplexed with bcl2fastq 2.20
Reads were aligned to the hg38 genome reference using STAR 2.7.7a in two-pass mode with Gencode v38 annotations.
Per-gene counts were generated with STAR's “--quantMode GeneCounts” option.
Second-strand counts for genes annotated as  protein coding, polymorphic pseudogenes, or lncRNAs were retained and combined into a single gene-count matrix for all samples.
Assembly: hg38
Supplementary files format and content: Tab-delimited text includes raw per-gene counts for each sample

growth_protocol: At the time of the BAL procedure, 6 mL of blood were collected in EDTA tubes for plasma isolation and 2.5 mL of blood in PAXgene tubes (QIAGEN, Germantown, MD). PAXgene tubes were stored according to the package insert.

extract_protocol:
MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit and GLOBINclear (Thermo Fisher Scientific, Bothell, WA) to deplete alpha and beta globin mRNA from whole blood samples according to the package inserts. DNase treatment was incorporated into both BAL and blood RNA extractions to reduce contamination by genomic DNA.
The TruSeq RNA Exome kit was used to prepare cDNA libraries.

value: blood

tag: subgroup

value: Fungal

tag: hhv6 in_bal

value: No

tag: hhv6 in_blood


title: PaxWholeBlood, pre-BAL[96588F]

value: Viral

value: Yes


title: PaxWholeBlood, pre-BAL[93211P]


title: PaxWholeBlood, pre-BAL[89797X]

value: IPS


title: PaxWholeBlood, pre-BAL[89756Q]


title: PaxWholeBlood, pre-BAL[87190M]


title: PaxWholeBlood, pre-BAL[88732O]


title: PaxWholeBlood, pre-BAL[82746V]


title: PaxWholeBlood, pre-BAL[95183K]

value: Bacterial


title: PaxWholeBlood, pre-BAL[79430V]


title: PaxWholeBlood, pre-BAL[78674Q]


title: PaxWholeBlood, pre-BAL[77906K]


title: PaxWholeBlood, pre-BAL[84179Q]


title: Pt 11 - treatment-naïve biopsy

description:
J15179_11Bx_rsem_hg38.genes.results
expected_count.txt column name:  J15179_11Bx_rsem_hg38.genes.results

value: non-metastatic ccRCC


title: PaxWholeBlood, pre-BAL[72424R]


title: Pt 10 - post-treatment nephrectomy

description:
J15179_10NxT_rsem_hg38.genes.results
expected_count.txt column name:  J15179_10NxT_rsem_hg38.genes.results


title: PaxWholeBlood, pre-BAL[74740Y]


title: PaxWholeBlood, pre-BAL[63921N]


title: PaxWholeBlood, pre-BAL[68603I]


title: PaxWholeBlood, pre-BAL[61109B]


title: PaxWholeBlood, pre-BAL[60100D]


title: Pt 9 - treatment-naïve biopsy

description:
C17_6037Bx_rsem_hg38.genes.results
expected_count.txt column name:  C17_6037Bx_rsem_hg38.genes.results


title: PaxWholeBlood, pre-BAL[70935R]


title: PaxWholeBlood, pre-BAL[57672S]


title: PaxWholeBlood, pre-BAL[54695J]


title: Pt 1 - treatment-naïve biopsy

description:
J15179_01Bx_rsem_hg38.genes.results
expected_count.txt column name:  J15179_01Bx_rsem_hg38.genes.results


title: PaxWholeBlood, pre-BAL[57430W]


title: PaxWholeBlood, pre-BAL[51519N]


title: PaxWholeBlood, pre-BAL[51963G]


title: PaxWholeBlood, pre-BAL[49204H]


title: PaxWholeBlood, pre-BAL[49466I]


title: PaxWholeBlood, pre-BAL[49131J]


title: PaxWholeBlood, pre-BAL[77313L]


title: PaxWholeBlood, pre-BAL[45456O]


title: PaxWholeBlood, pre-BAL[44264M]


title: PaxWholeBlood, pre-BAL[37214X]


title: PaxWholeBlood, pre-BAL[39317S]


title: PaxWholeBlood, pre-BAL[34799V]


title: PaxWholeBlood, pre-BAL[34953D]


title: PaxWholeBlood, pre-BAL[33469P]


title: PaxWholeBlood, pre-BAL[34471A]


title: PaxWholeBlood, pre-BAL[24030A]

value: Not tested


title: PaxWholeBlood, pre-BAL[24905K]


title: PaxWholeBlood, pre-BAL[28434H]


title: PaxWholeBlood, pre-BAL[19683Y]


title: PaxWholeBlood, pre-BAL[21618M]


title: PaxWholeBlood, pre-BAL[61101F]


title: PaxWholeBlood, pre-BAL[29258V]


title: PaxWholeBlood, pre-BAL[19501V]


title: PaxWholeBlood, pre-BAL[13246K]


title: PaxWholeBlood, pre-BAL[12541J]


title: PaxWholeBlood, pre-BAL[49672J]


title: PaxWholeBlood, pre-BAL[4064]


title: PaxWholeBlood, pre-BAL[3219]


title: PaxWholeBlood, pre-BAL[3418]


title: PaxWholeBlood, pre-BAL[38986Y]


title: miRNA, placebo, D3 286_S88_L001

city: Göteborg

first: Björn

last: Andersson

address: Sahlgrenska akademin, Core Facilities, Box 413

department: Boinformatics and Data center

country: Sweden

institute: Univeristy of Gothenburg

description:
miRNA, placebo, D3
miRNA-seq

data_processing:
Adapters and indexes have been removed by using cutadapt v2.10.
Reads were aligned to GRCh38 by using bowtie2 v2.3.5.1.
Alignments were processed using samtools v1.9 to obtain a sorted bam-file which was used as input in HTSeq.count v0.13.0.
Counts were normalized by sequencing depth, dividing each sample with the column sums and multiplying them by 1 M. Baseline adjustment was performed individually by dividing the normalized data at each time point (day 1, 2, 3, and 7) by day 0 (e.g. day 1/day 0). All values were Log2-transfomed before further analyses. The R software v4.0.1 was used to perform normalization and baseline adjustment.
Assembly: GRCh38
Supplementary files format and content: txt file with normalized and log2 transformed counts

source_name: serum-derived extracellular vesicles

extract_protocol:
extracellular vesicles (EV)-RNAs, including miRNAs, were isolated by using the PAXgene blood miRNA kit (PreAnalytiX). This kit guarantees the extraction of intracellular RNA and miRNA upon cell lysis and stabilization of intracellular RNA during whole blood collection in PAXgene blood RNA tubes (PreAnalytiX). The elutes were quantified with a Qubit fluorometer (ThermoFisher Scientific) by using the RNA Broad Range assay kit (ThermoFisher Scientific). RNA quality was assessed by using Agilent RNA (15nt) fragment analysis (Agilent).
Libraries were prepared using the NEBNextâ Multiplex Small RNA Library Prep Kit for Illumina (New England BioLabs) (Index Primers 1-48, #7560S). Their quality and yield were measured by Agilent HS NGS fragment analysis (Agilent). The final products have approximate size of 150 bp. The 1.1 nM libraries, derived from the WB RNAs, were sequenced using the NovaSeq 6000 sequencer with a 150 bp paired-end protocol. Between 9 and 41 million reads were obtained for each sample (average of 17 million reads per sample).

value: serum-derived extracellular vesicles

value: placebo

tag: time


title: miRNA, placebo, D7 288_S90_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D2 285_S87_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D7 288_S90_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D4 287_S89_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D2 285_S87_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D1 284_S86_L001

description:
miRNA, placebo, D1
miRNA-seq


title: PaxWholeBlood, pre-BAL[2513]


title: miRNA, placebo, D0 283_S85_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D7 282_S84_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D0 283_S85_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D4 281_S83_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D7 282_S84_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D3 280_S82_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D1 278_S80_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D3 280_S82_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D1 278_S80_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D4 281_S83_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D3 286_S88_L002

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D2 279_S81_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D7 276_S78_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D0 277_S79_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D0 277_S79_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D4 287_S89_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D4 275_S77_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D1 284_S86_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D3 274_S76_L002

description:
miRNA, placebo, D3
miRNA-seq


title: PaxWholeBlood, pre-BAL[21196A]


title: miRNA, placebo, D2 273_S75_L002

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D1 272_S74_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D4 275_S77_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D1 272_S74_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D3 274_S76_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D2 273_S75_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D0 271_S73_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D7 276_S78_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D2 279_S81_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D7 270_S72_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D0 271_S73_L001

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D2 267_S69_L001

description:
miRNA, placebo, D2
miRNA-seq


title: miRNA, placebo, D1 266_S68_L001

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D3 268_S70_L001

description:
miRNA, placebo, D3
miRNA-seq


title: miRNA, placebo, D7 270_S72_L002

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D4 269_S71_L002

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D4 269_S71_L001

description:
miRNA, placebo, D4
miRNA-seq


title: miRNA, placebo, D0 265_S67_L002

description:
miRNA, placebo, D0
miRNA-seq


title: miRNA, placebo, D1 266_S68_L002

description:
miRNA, placebo, D1
miRNA-seq


title: miRNA, placebo, D7 264_S66_L001

description:
miRNA, placebo, D7
miRNA-seq


title: miRNA, placebo, D7 264_S66_L002

description:
miRNA, placebo, D7
miRNA-seq