title: CH12_RNAseq_Rif1KO_clone2_rep3

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
RNA-seq
Read alignment: 3' adaptors or reads were removed using cutadapt  (v1.4.2, Read1: cutadapt --match-read-wildcards -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) and trimmed reads with a length of less than 18bp were discarded.
The trimmed reads were filtered with a contaminants database consisting of rDNA sequences (gi|374088139, gi|38176281) with bowtie2(v2.1.0 --very-sensitive-local).
The recovered non matching reads were aligned to the genome/transcriptome using STAR-align (v2.4.2a, STAR  --outSAMstrandField None --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverLmax 0.1 --outFilterMismatchNmax 10 --outFilterScoreMinOverLread 0.30 --outFilterMatchNminOverLread 0.30 --outFilterMatchNmin 30 --chimSegmentMin 15 --quantMode TranscriptomeSAM --chimJunctionOverhangMin 15 --twopassMode Basic --outSAMtype SAM --outSAMattributes All --outReadsUnmapped Fastx intronMotif --alignIntronMax 200000  --outSJfilterIntronMaxVsReadN 10000 20000 30000 50000 --outSJfilterOverhangMin 20 12 12 12 --outFilterType BySJout --alignMatesGapMax 0  --outFilterMultimapNmax 20).
The STAR-index used for alignment was generated from the combination of the mouse genome build NCBI m37 (GCA_000001635.18) and a transcriptome GTF file created from all refGenes and ensGenes gtfs downloaded from the UCSC Table Browser on the 1. March 2014.
Unique mappers from the resulting BAM file were used to create unstranded, stranded and reverse stranded coverage tracks for visualisation using bedtools (v2.27, bedtools genomecov -split -bg, bedtools genomecov  -split -bg -strand '+' ,bedtools genomecov -split -bg -strand '-') and bedGraphToBigWig from the kent-tools (bedGraphToBigWig v4, bedGraphToBigWig -blockSize=256 -itemsPerSlot=1024).
Normalised coverage tracks were created by dividing the coverage at each position with the total number of aligned reads per million.
Differential gene expression analysis: Read counts for genes were quantified using featureCounts v2.0.0.
As a reference, we downloaded all mm9 refSeq genes from the UCSC table browser (https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/genes/) on February 28, 2020.
In addition, we downloaded the Igh, Igk and Igl gene Ensembl Gene IDs from IMGT (http://www.imgt.org, August 11, 2020) and extracted the corresponding genes from Gencode M25 (www.gencodegenes.org) and lifted them over to mm9 coordinates and added them in addition to the Elambda 3_1 enhancer.
Differential gene expression analysis was performed with DESeq2 v1.22.2 and shrinking log2-foldchanges with ashr v2.2-47.
Assembly: NCBI mm9
Supplementary files format and content: Tab-delimited table with TPMs and DESeq2 log2-foldchanges, adjusted p-values and control TPMs

growth_protocol: RNA-seq was performed on CH12 and two independent RIF1-deficient (RIF1-/-) CH12 clonal derivatives 30 with three replicates. Cells were expanded in complete RPMI and 1 million cells were collected by centrifugation

extract_protocol:
RNA was extracted with TRIzol (Invitrogen) according to manufacturer’s instructions.
TruSeq RNA Library Prep Kit v2 (Illumina) was used to prepare a whole-transcriptome sequencing library

value: Rif1KO clone2


title: E2_ 5 and 6

status: Public on Jun 13 2023

type: SRA

city: Dallas

first: Philip

last: Shaul

state: TX

address: 5323 Harry Hines Blvd.

department: Pediatrics

country: USA

institute: UT Southwestern

library_source: transcriptomic

data_processing:
Raw data were de-multiplexed and converted to fastq files using bcl2fastq (v2.17)
The fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Sequencing reads were mapped to mm10 reference genome (from igenomes) using STAR (v2.5.3a), counted using featureCounts (subread/v1.6.0)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with raw read counts calculated using igenomes gtf file

molecule: polyA RNA

organism: Mus musculus

source_name: gastrocnemius and soleus

extract_protocol:
Skeletal muscle tissue was harvested and homogenized. Immunoprecipitation with GFP antibody was used to isolate GFP-taged ribosomes (only found in endothelial cells) and their associated mRNA species. mRNA was purified and used for library preparation. Libraries were then sequenced on an Illumina sequencer using a 400MR Illumina chip.
mRNA libraries were prepared for sequencing using SMARTer Stranded total RNA sample prep kit (TAKARA), which is Illumina compatible.

treatment_protocol: 4 week old B6.129S4-Gt(ROSA)26Sorfm1(CAG-EGFP/Rpl10a; birA/Wtp/J mice were treated with either placebo OR 17β-estradiol pellets for 4 weeks.

tag: genotype

tag: treatment

value: 17Beta-estradiol pellets

tag: treatment time

value: 4 weeks

tag: tissue

value: whole skeletal muscle

tag: antibody

value: GFP


title: C11-71

city: Ames

first: James

last: Koltes

state: Iowa

address: 1221 Kildee Hall

department: Department of Animal Science

institute: Iowa State University

data_processing:
Adapter and low-quality bases were removed using the bbduk.sh program in BBtools software
Reads less than 20 bases and quality score (Phred + 33) ≥ 20 were filtered out
Reads were aligned against  the reference genome (Suscrofa11.1) using STAR and the RNA quantification (Counts) using FeatureCounts
Assembly: Pig/Suscrofa11.1
Supplementary files format and content: tab-delimited text files raw counts values for each Sample

molecule: total RNA

organism: Sus scrofa

source_name: Liver

extract_protocol:
Total RNA was isolated and purified from jejunum mucosa, kidney cortex, and liver tissues using the Qiagen RNeasy Plus Mini Kit (Germantown, MD, USA) per the manufacturer’s instructions. For the longissimus dorsi muscle samples, the Qiagen RNeasy Fibrous Tissues Mini Kit (Germantown, MD, USA) was utilized for total RNA isolation and purification per the manufacturer’s instructions.
RNA libraries were constructed using 3’ mRNA-seq QuantSeq technology (Lexicogen, 194 Greenland, NH).

treatment_protocol: Two dietary treatments were evaluated using different concentrations of xylose: a semi-purified xylose-free diet (CTL) and the same diet with 8% D-xylose (DuPont Nutrition & Health, Copenhagen, Denmark)

value: Liver

value: Xylose treatment

tag: diet supplementation

value: 8percent D-xylose


title: CH12_RNAseq_Rif1KO_clone2_rep2


title: E2_ 3 and 4


title: CH12_RNAseq_Rif1KO_clone2_rep1


title: Donor 40389, Minimal residual disease

city: Galway

first: Eva

last: Szegezdi

address: University Road

country: Ireland

institute: University of Galway

description:
10X Genomics
40389_MRD

library_source: transcriptomic single cell

data_processing:
Reads were aligned and quantified using CellRanger v6.0.0. Cell type annotations were predicted using the dataset from Granja et. al. (GSE139369) as a reference.
Assembly: hg38
Supplementary files format and content: Processed data is provided as tab-delimited text files. For each sample there are two files: a cell (rows) x gene (columns) count matrix and a metadata file with cell type annotations for each cell.

organism: Homo sapiens

source_name: Bone marrow aspirate

extract_protocol:
Bone marrow aspirates were obtained from The Finnish Haematology Registry and Clinical Biobank. The mononuclear cell fraction was isolated using Ficoll density gradient separation.
Cell counting and viability assessments were conducted using To-Pro-3 viability dye. Thereafter, GEM generation & barcoding, reverse transcription, cDNA amplification and 3’ gene expression library generation steps were all performed according to the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Single Index) User Guide (10x Genomics CG000204 Rev D) with all stipulated 10x Genomics reagents.

value: Bone marrow aspirate

tag: subject id

value: Donor 40389

tag: time point

value: Minimal residual disease


title: Donor 4978, Relapse

description:
10X Genomics
4978_R

value: Donor 4978

value: Relapse


title: G06-58


title: E2_ 1 and 2


title: C10-70


title: Donor 40389, Diagnosis

description:
10X Genomics
40389_Dg

value: Diagnosis


title: PL_5 and 6

value: Placebo pellets


title: Donor 4978, Diagnosis

description:
10X Genomics
4978_Dg


title: CH12_RNAseq_Rif1KO_clone1_rep2

value: Rif1KO clone1


title: Donor 3904, Minimal residual disease

description:
10X Genomics
3904_MRD

value: Donor 3904


title: C05-76


title: CH12_RNAseq_Rif1KO_clone1_rep1


title: CH12_RNAseq_Rif1KO_clone1_rep3


title: C03-73


title: PL_1 and 2


title: Donor 40389, Relapse

description:
10X Genomics
40389_R


title: Donor 3904, Relapse

description:
10X Genomics
3904_R


title: PL_ 3 and 4


title: C07-72


title: Donor 3904, Diagnosis

description:
10X Genomics
3904_Dg


title: C02-78


title: MEF, Ctrl, replicate1, RNA-seq

city: Shinjuku

first: Taketaro

last: Sadahiro

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver 10.1.1, Qiagen).
Reads were mapped to mouse reference genome (mm10).
CLC Main Workbench(Ver 21.0.4, Qiagen) was used for the downstream analysis.
Supplementary files format and content: Microsoft Excel file  with raw counts, normalized expression values and transformed values for every gene

source_name: mouse embryonic fibroblast

extract_protocol:
For MEF, RNA was extracted using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012). For whole heart, mice were sacrificed by CO2 inhalation, and hearts were immediately cannulated and perfused with cold PBS. After the heart was harvested, the atria and valves were removed, and  RNA was extracted using Trizol reagent.
500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420)

value: mouse embryonic fibroblast

tag: time

value: 4 weeks after transduction

value: ICR

value: MEF


title: Donor 3853, Relapse

description:
10X Genomics
3853_R

value: Donor 3853


title: CH12_SNSseq_WT_rep2

description: SNS-seq

library_source: genomic

data_processing:
library strategy: SNS-seq
Reads were quality and adaptor trimmed with trim_galore v0.6.4 and cutadapt v2.6 with a length filter of 18bp
Trimmed reads were aligned to the mouse genome (mouse genome build UCSC mm9) using bowtie v1.2.3
rreplicate peak sets for each condition were overlapped with BEDTools intersect 2.27.1 using default parameters retaining only those peaks that were found in both replicates
retained peaks were then clustered by genome-wide median interpeak distance with ClusterScan 0.2.1 using -n 2 and only peaks that are part of a cluster were retained
filtered peak sets were then merged merged with BEDTools merge 2.27.1
Assembly: mm9
Supplementary files format and content: CH12_unstimulated_IS.bed is a BED file containing the genomic positions of the merged initiation sites for Rif1KO and WT

molecule: genomic DNA

growth_protocol: CH12 cells cultured in complete RPMI medium wit IL4/CD40/TGF beta stimulation.

extract_protocol:
short nascent DNA was enriched via size selection and lamda exonuclease digestion
Libraries were prepared following standard Illumina protocols
Genomic DNA was extracted and short nascent DNA was enriched via size selection and lamda exonuclease digestion

tag: cell line

value: WT


title: G10-67

value: Liver

value: Control

value: Xylose-free (0percent)


title: CH12_SNSseq_WT_rep1

description: SNS-seq


title: Donor 3853, Diagnosis

description:
10X Genomics
3853_Dg

value: Bone marrow aspirate


title: CH12_RNAseq_WT_rep2


title: CH12_SNSseq_Rif1KO_rep2

description: SNS-seq


title: G08-65


title: G07-66


title: CH12_RNAseq_Rif1KO_shMcm6_rep3

tag: infection


title: CH12_RNAseq_WT_rep3


title: CH12_RNAseq_WT_rep1


title: CH12_SNSseq_Rif1KO_rep1

description: SNS-seq


title: Donor 3822, Relapse

description:
10X Genomics
3822_R

value: Donor 3822


title: G05-63


title: G04-61


title: CH12_RNAseq_Rif1KO_shMcm6_rep2


title: Donor 1886, Minimal residual disease

description:
10X Genomics
1886_MRD

value: Donor 1886

value: Minimal residual disease


title: Donor 1886, Diagnosis

description:
10X Genomics
1886_Dg

value: Diagnosis


title: CH12_RNAseq_Rif1KO_shMcm6_rep1


title: G02-59


title: CH12_RNAseq_Rif1KO_shLacZ_rep3

value: shLacZ


title: Donor 1886, Relapse

description:
10X Genomics
1886_R

value: Relapse


title: Donor 1216, Relapse

description:
10X Genomics
1216_R

value: Donor 1216


title: C12-77


title: 15203X1 Wild-type (day 13)

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

data_processing:
Raw base call files (BCL) from Illumina 10x Genomics Single-Cell Gene Expression were demultiplexed uing the Cell Ranger mkfastq pipeline.
The Fastq files were aligned to the refdata-cellranger-mm10-1.2.0 mouse reference dataset from 10X genomics using cellranger count version 2.0.2.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrices from cellranger count

source_name: CD45+ brain immune cells

extract_protocol:
Brain and spinal cord tissues were dissociated using scissors and forceps and processed on ice. After a percoll gradient, cells were stained with DAPI and APC-conjugated CD45 for 15 minutes on ice in PBS containing 2 mM EDTA and 0.5% BSA. Live CD45+ cells were sorted via BD FACSAria cell sorter and washed once in PBS containing 0.04% BSA. Samples were then processed for SCseq via a 10× platform according to the manufacturer’s instructions (10× Genomics).
Single-cell 3' RNA-Sequencing

tag: strain

value: brain

tag: timepoint

value: day 13


title: CH12_RNAseq_Rif1KO_shLacZ_rep1


title: 15232X2 miR-155KO (day 21)

value: day 21


title: 15454X2 miR-155KO (day 0)

value: day 0


title: Donor 1216, Minimal residual disease

description:
10X Genomics
1216_MRD


title: CH12_RNAseq_Rif1KO_shLacZ_rep2


title: C08-74


title: Donor 3822, Diagnosis

description:
10X Genomics
3822_Dg


title: CH12_SNSseq_Rif1KO_shMcm6_rep2

description: SNS-seq


title: CH12_SNSseq_Rif1KO_shMcm6_rep1

description: SNS-seq


title: 15454X1 Wild-type (day 0)


title: C06-69


title: HuTh17_Veh

city: Winston-Salem

first: Qianqian

last: Song

state: NC

address: 1 Medical Center Boulevard

department: Cancer Genomics and Precision Oncology

institute: Wake Forest Baptist Comprehensive Cancer Center

data_processing:
Run cellranger mkfastq on the Illumina BCL output folder to generate FASTQ files.
Run cellranger count on each library that was demultiplexed by cellranger mkfastq.
Run cellranger aggr to aggregate multiple libraries from a single experiment that were analyzed by cellranger count.
Assembly: mm10 (CLF_CR, CLF_TC, Veh_CR, Veh_TC) and GRCh38 (HuTh17_CLF and HuTh17_Veh)
Supplementary files format and content: tab-delimited text files include UMI counts for each Sample …

source_name: P6 Terminal ileum and acending colon biopsies

extract_protocol:
Cells were isolated from colonic tissues via enzymatic digestion and density gradient protocol. Isolated cells were purified for Th17 cells by sorting RORgt-EGFP+ cells via FACS prior to extraction. Viable cells (mean 83.4 ± 9.9%, n = 5) in suspensions averaging 995 ± 267 cell/µl were loaded into wells of a 10X Chromium single-cell capture chip targeting a cell recovery rate of 2,000 – 3,000 cells. Single-cell gel beads in emulsion (GEMs) were created on a Chromium Single Cell Controller and scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead kit according to the manufacturer's protocol (10× Genomics).
Single-cell gel beads in emulsion (GEMs) were created on a Chromium Single Cell Controller and scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead kit according to the manufacturer's protocol (10× Genomics) - following these steps: (1) end repair and A-tailing; (2) adapter ligation; (3) post-ligation cleanup with SPRIselect; (4) sample index PCR and cleanup.  The barcode sequencing libraries were quantified using the Qubit 3.0 (Thermo Fisher, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were treated with CLF or vehicle intraperitoneally every other day at human equivalent dose starting at day 1 (CR) or day 14 (TC). Human biopsies were incubated for 18 hours in CLF at 1 uM or vehicle at 37F in media and stimulated with 5 ng/ml PMA and 1 uM Ionomycin prior to extraction.

tag: model disease

value: Inflammatory bowel disease (Crohn's Disease)

tag: Sex

value: Male

tag: age

value: 53 Years


title: C09-75

value: Liver

value: Control


title: CH12_SNSseq_Rif1KO_shLacZ_rep2

description: SNS-seq


title: 15203X2 miR-155KO (day 13)


title: 15232X1 Wild-type (day 21)

value: WT


title: C01-80

value: Xylose-free (0percent)


title: CH12_SNSseq_Rif1KO_shLacZ_rep1

description: SNS-seq


title: C04-79


title: HuTh17_CLF


title: Input, SMS-CTR, for H3K9me3, rep1

city: Columbus

first: Benjamin

last: Stanton

state: Ohio

address: 700 Children's Drive

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

data_processing:
All ChIP data were processed with ENCODE ChIP-seq pipeline (v2.1.2) with chip.xcor_exclusion_range_max set at 25
ENCODE ChIP-seq alignment: normalized paired-end  fastqs were aligned with bowtie2 aligner to human genome UCSC hg38, with parameters bowtie2 -X2000 --mm
ENCODE ChIP-seq read filtering: black listed region, unmapped, mate unmapped, not primary alignment, multi-mapped, low mapping quality (MAPQ<30), duplicate reads and PCR duplicate were removed
ENCODE ChIP-seq peak calling: Peaks were called with MACS2, with parameters -p 1e-2 --nomodel --shift 0 --extsize ${FRAGLEN} --keep-dup all -B –SPMR. IDR analyses were performed on peaks from replicate samples, with threshold 0.05
Assembly: hg38
Supplementary files format and content: peak text files, BED format
Supplementary files format and content: bigwig files, signals represent fold change over Input

source_name: RD

growth_protocol: RH4, RH30, RD, SMS-CTR, and C2C12 were grown in DMEM supplemented with 10% FBS.

extract_protocol:
For spike-in normalized ChIP-seq, human RMS cells and mouse C2C12 cells were fixed in 1% formaldehyde for 10 minutes before quenching with 125 mM glycine. Cells were combined in a ratio of 3 human:1 mouse cell equivalents for each experiment prior to sonication. Sonicated chromatin was immunoprecipitated with antibodies against H3K27ac (Active Motif #39133), H3K9me3 (Active Motif #39062), MYOD1 (CST #13812), or CTCF (Millipore #07-729). Input and ChIP-enriched DNA was decrosslinked and purified using Qiagen MinElute PCR Purification columns prior to library preparation.
H3K27ac, MYOD1, and CTCF ChIP and Input DNA libraries were prepared by blunt end repair using the Lucigen End-It DNA End-Repair Kit, 3’ A-tailing by Klenow fragment (3’-5’ exo-) (NEB), adaptor ligation by T4 DNA ligase(NEB), and size selection on an E-Gel 2% EX agarose gel. Libraries were amplified with barcoded primers and isolated from unreacted primers by gel purification. Decrosslinked H3K9me3 ChIP and Input DNA was sonicated to enrich fragments 200-500-bp. Library prep was then performed without further size selection. Excess adapter and unused primers were removed with AmpureXP beads.  Libraries were sequenced on the HiSeq4000 or NovaSeq6000 platform running in PEx150bp mode.

value: RD

value: Input

tag: antibody vendor/catalog


title: F12-120

source_name: Kidney

value: Kidney

value: Xylose treatment

value: 8percent D-xylose


title: H3K9me3, RD, rep1

value: Active Motif, 39062


title: CH12_HiC_Rif1KO_shMcm6

description: HiC

data_processing:
Hi-C
Raw paired-end reads were controlled for quality and adapters were removed with trim_galore 0.6.2 with a quality cutoff of 20
Trimmed read pairs were processed with HICUP 0.7.3 using ^GATC,MboI as restriction enzyme and mouse mm9 as reference genome
Aligned, filtered and deduplicated read pairs were converted to pairix with cooler csort 0.8.3
Resulting pairix files were then used to generate a 5kb initial contact matrix using cooler cload pairix 0.8.3 with canonical chromosome sizes of mm9 and cooler zoomify 0.8.3 was used to generate resolutions of 10kb, 20kb, 25kb, 50kb, 100kb, 200kb, 250kb, 500kb, 1Mb
Each resolution was then balanced using genome-wide KR (0.05, part of HiCExplorer) and IC (part of cooler 0.8.3) using default arguments and saved into a multicooler file
Similarly, juicer_tools 1.22.01 was used to generate hic files of the same resolutions and balanced with GW_KR for subsequent loop calling
In addition, HOMER 4.10 was used to compute compartment signals by first generating a ditag directory from HICUP results using makeTagDirectory. Subsequently, compartment signals were computed with runHiCpca.pl with -res 20000 -window 200000 -genome mm9 using the RefSeq gene annotation for mm9 as markers of the active compartment. TADs were called with findTADsAndLoops.pl find with -res 5000 -balance -window 50000 -genome mm9 using known duplications for mm9 (downloaded from UCSC) as bad regions.
Assembly: UCSC mm9
Supplementary files format and content: Multicoolers contain the raw contact matrixes as well as balancing weights for KR and IC algorithms for resolutions of 5kb, 10kb, 20kb, 25kb, 50kb, 100kb, 200kb, 250kb, 500kb, 1Mb. Balancing weights for each resolution were saved in the bins table as 'weight' (KR) and 'ICE' (IC) column, respectively
Supplementary files format and content: hic files contain the raw contact matrixes as well as balancing weights for GW_KR resolutions of 5kb, 10kb, 20kb, 25kb, 50kb, 100kb, 200kb, 250kb, 500kb, 1Mb
Supplementary files format and content: The first principal component as computed by homer was converted to bigWig with sort -k1,1 -k2,2n; bedGraphToBigWig (UCSC kent_tools/20190507-linux.x86_64) with a chromsize file containing only mm9 canonical chromosomes

extract_protocol:
DNA from crosslinked nuclei was digested with restriction enzyme, biotin filled ligated and streptavidin enriched
Libraries were prepared following standard Illumina protocols

tag: cell type

value: CH12 Rif1KO cells


title: TCC-3 - Serum - TCC

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
Reads were trimmed from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15. Reads shorter than 14 nt were removed.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings.
The human miRNAs were annotated and quantified using two methods called the "knowledge-based" and "position-based". miRNAs whose assigned arms were derived from the "position-based" methodology were indicated in italics.
The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Assembly: hg38
Supplementary files format and content: Matrix table with the raw mature miRNA read counts for each sample

source_name: Serum

extract_protocol:
The pooled serum samples were centrifuged at 16000rcf in order to remove debris, platelets or cells, and RNA was extracted from 200 µl, using the Qiagen miRNeasy kit (Qiagen GmbH, Hilden, Germany), following the manufacturer’s instructions. Syn-cel-miR-39 spike-in synthetic RNA (Qiagen GmbH, Hilden, Germany) was added to monitor extraction efficiency.
RNA samples (6 µl for each pool) were used for library generation using the NEBNext Multiplex Small RNA Prep (New England Biolabs, Ipswich, Massachussets, USA), and sequenced on a single-read flow cell by bridge amplification and 75 cycles sequencing-by-synthesis on the Illumina NextSeq550 platform (Illumina Inc., San Diego, California, USA).

value: Serum

tag: group

value: traditional combustion cigarettes (TCCs)


title: TCC-2 - Serum - TCC


title: CH12_HiC_Rif1KO_shLacZ

description: HiC

tag: treatment

value: shLacZ


title: TCC-1 - Serum - TCC

tag: tissue


title: F11-34


title: Input, RD, for H3K9me3, rep1

source_name: SMS-CTR

value: SMS-CTR

tag: antibody


title: F09-35

tag: diet supplementation


title: priB_Rif1WT_ChIPseq_rep2

data_processing:
ChIP-seq
Raw reads were trimmed with trim_galore v0.6.4 (https://github.com/FelixKrueger/TrimGalore) setting minimum length to 18 bases and default arguments otherwise
The trimmed reads were aligned to aligned to the mm9 reference genome with bowtie v1.0.0 with -S --trim5 0 --trim3 0 -v 2 --best --strata --tryhard -m 1 --phred33-quals --chunkmbs 256
Genome coverage tracks were computed with deeptools bamCoverage v3.3.0 using command-line parameters --normalizeUsing CPM --exactScaling –binSize 50 and –ignoreDuplicates
Log2 ratio tracks were computed with deeptools bamCompare v3.3.0 using command-line parameters --scaleFactorsMethod readCount --operation log2 --pseudocount 1 –binSize 50 –ignoreDuplicates.
RIF1 narrow and broad peaks were called for each replicate with MACS v2.2.6, RIF1 associated domains (RADs) were called using EDD v1.1.19. RADs, narrow and broad peaks and domains were merged using bedtools v2.27.1 and only those peaks called in both replicates were retained for downstream analysis
Assembly: mm9
Supplementary files format and content: bedfile contains Rif1 narrow and broad peaks as well as Rif1 assiciated domains called in both replicates
Supplementary files format and content: bigWigs contain either genome coverage of Rif1 ChIPseq or log2 ratios between Rif1 ChIP and input

source_name: priB

growth_protocol: primary B cells were isolated from Rif1FH/FH and C57BL/6 (Rif1WT/WT) mice spleens using anti-CD43 MicroBeads (Miltenyi Biotec) and expanded in complete RPMI containing 5 µg/ml LPS (Sigma-Aldrich) and 5 ng/ml mouse recombinant IL-4 (Sigma-Aldrich) to allow B cell activation and class switch recombination to IgG1. B cells were harvested 72h after activation and 4 x 10^7 cells

extract_protocol:
Chromatin immunoprecipitation was performed as described Foti et al. 2021. In summary, primary B cells were isolated from Rif1FH/FH and C57BL/6 (Rif1WT/WT) mice spleens using anti-CD43 MicroBeads (Miltenyi Biotec) and expanded in complete RPMI containing 5 µg/ml LPS (Sigma-Aldrich) and 5 ng/ml mouse recombinant IL-4 (Sigma-Aldrich) to allow B cell activation and class switch recombination to IgG1. B cells were harvested 72h after activation and 4 x 107 cells were cross-linked by using 2 mM disuccinimidyl glutarate (ThermoFisher 20593) in PBS for 45 min and 1% formaldehyde for 5 min (Thermo Scientific 28908). The reaction was quenched with 0.125 M glycine. Cells were washed thrice with ice-cold PBS and lysed in SDS lysis buffer. Chromatin fragmentation was performed using a Covaris E220 sonicator to obtain fragments between 200 and 600 bp. Chromatin was quantified with a ND-1000 NanoDrop spectrophotometer. Immunoprecipitation was performed with 0.5 μg of anti-HA antibody (Santa Cruz sc-7392) and 50 µl of Dynabeads protein G (Thermofisher 10003D) and 25 μg chromatin
ChIP libraries were prepared by NEBNext ultra II DNA library preparation kit (NEB E7645L) and sequenced on one lane of a NovaSeq 6000 (Illumina) machine
4 x 10^7 cells were cross-linked by using 2 mM disuccinimidyl glutarate  in PBS for 45 min and 1% formaldehyde for 5 min . The reaction was quenched with 0.125 M glycine. Cells were washed thrice with ice-cold PBS and lysed in SDS lysis buffer. Chromatin fragmentation was performed using a Covaris E220 sonicator to obtain fragments between 200 and 600 bp. Chromatin was quantified with a ND-1000 NanoDrop spectrophotometer. Immunoprecipitation was performed with 0.5 μg of anti-HA antibody (Santa Cruz sc-7392) and 50 µl of Dynabeads protein G (Thermofisher 10003D) and 25 μg chromatin

value: primary B cells

tag: genotype

value: C57BL/6 (Rif1WT/WT)

value: anti-CD43 MicroBeads


title: H3K9me3, RH30, rep1


title: HNBC-3 - Serum - HNBC

value: heat-not-burn cigarettes (HNBCs)


title: Donor 1216, Diagnosis

description:
10X Genomics
1216_Dg

value: Bone marrow aspirate

tag: subject id

value: Donor 1216

tag: time point

value: Diagnosis


title: Input, RH30, for H3K9me3, rep1

tag: cell line

value: Input


title: H3K9me3, SMS-CTR, rep1


title: F06-40

value: Kidney


title: priB_Rif1WT_ChIPseq_rep1


title: HNBC-2 - Serum - HNBC


title: HNBC-1 - Serum - HNBC


title: MYOD, RD, rep1

value: RD

value: MYOD

value: Cell Signaling, 13812 (D8G3)


title: MYOD, SMS-CTR, rep1


title: F01-56

value: Xylose treatment

value: 8percent D-xylose


title: NS-3 - Serum - NS

value: Serum

value: non-smokers (NS)


title: priB_Rif1FH_ChIPseq_rep2


title: priB_Rif1FH_ChIPseq_rep1


title: NS-2 - Serum - NS


title: MYOD, RH4, rep1


title: 15297X30 Abcb10 knockout cells Day 5 biol rep 5

first: W. Zac

last: Stephens

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3
Assembly: mm10
Supplementary files format and content: featureCount output files combined into a single tab-delimited raw count matrix

source_name: MEL

growth_protocol: DMEM with 1.0 mM Na pyruvate, 1X Glutamax, 1X non-essential amino acids, 100 units/ml penicillin, 100 ug/ml streptomycin. 37 C, 5% CO2

extract_protocol:
Zymo Research DirectZol RNA Extraction
RNA was processed with Ribo-Zero Globin and stranded RNA seq libraries were prepared with Illumina TruSeq Stranded Total RNA Library Prep Gold.

value: MEL

value: Erythroleukemia cells

value: Abcb10 knockout

value: 1.5% DMSO

tag: time

value: 5 days treatment


title: MYOD, RH30, rep1


title: 15297X29 Abcb10 knockout cells Day 5 biol rep 4


title: B10-52


title: 15297X28 Abcb10 knockout cells Day 5 biol rep 3


title: B07-85


title: 15297X27 Abcb10 knockout cells Day 5 biol rep 2


title: CTCF, RH30, rep2

value: CTCF

value: Millipore, 07-729


title: CTCF, SMS-CTR, rep2

value: SMS-CTR


title: CTCF, RD, rep2


title: B05-83


title: B03-122


title: 15297X26 Abcb10 knockout cells Day 5 biol rep 1


title: B02-49


title: CTCF, RH4, rep2


title: 15297X25 WT MEL cells Day 5 biol rep 5

value: WT


title: F03-33

value: Kidney


title: B11-121


title: F10-55

value: Control

value: Xylose-free (0percent)


title: CTCF, SMS-CTR, rep1


title: 15297X24 WT MEL cells Day 5 biol rep 4


title: H12-sg-2_batch2

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

description: Derived from sequence batch #2

data_processing:
All raw sequence reads generated by Illumina HiSeq 2000 had been demultiplexed at Novogene as 2x150 bp reads aiming at 25 M reads;
RNA-seq data was aligned to GRCh38.p12 genome using STAR 2.7.10 and GENCODE v35;
ENSEMBL gene ids were used to serve as the unique gene identifiers. The raw count matrix was constructed by collecting the STAR output matrix of each sample and concatenating into one large tab-delimited text file.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text

extract_protocol: For RNA-Seq, at the day of harvesting the culture media was removed by aspiration and the cells were washed twice using 1 ml PBS each with aspiration. Subsequently, 600 µl of RLT Plus reagent was directly added into each well to homogenise cells in situ. Qiagen RNEasy plus kit was used for the extraction of total RNA according to the manufacturer’s protocol. Extracted RNAs were eluted into 50 µl of RNA-free water and the concentration was determined by nanodrop. Approximately 5 µg total RNA was recovered from each well. Total RNAs isolated by using MirVana kit (Thermofisher) were used in RNA-seq. After QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Subsequently, terminal repair and sequencing adaptor ligation were applied to the templates. The double-stranded cDNA library is completed through size selection and PCR enrichment.

value: Glutamatergic, NGN2-induced, day-20 neuron

value: 3x shRNA combined KD


title: H12-EGFP-3_batch2

description: Derived from sequence batch #2

value: EGFP shRNA ctrl


title: H12-sg-1_batch2

description: Derived from sequence batch #2


title: NS-1 - Serum - NS

value: Serum


title: H12-EGFP-1_batch2

description: Derived from sequence batch #2


title: 15297X23 WT MEL cells Day 5 biol rep 3


title: CTCF, RH30, rep1


title: H12-sg-3_batch2

description: Derived from sequence batch #2


title: F08-53


title: CTCF, RD, rep1

value: RD


title: F07-36


title: 15297X22 WT MEL cells Day 5 biol rep 2

value: MEL


title: B11-EGFP-3_batch2

description: Derived from sequence batch #2


title: CTCF, RH4, rep1


title: Input, RH4, for both reps of CTCF, MYOD rep1 SEG0228

value: Input


title: B11-EGFP-2_batch2

description: Derived from sequence batch #2


title: F04-38


title: 15297X21 WT MEL cells Day 5 biol rep 1

value: Erythroleukemia cells


title: 15297X20 Abcb10 knockout cells Day 2 biol rep 5

value: Abcb10 knockout

value: 1.5% DMSO

value: 2 days treatment


title: B11-EGFP-1_batch2

description: Derived from sequence batch #2


title: F02-54


title: Input, RD, for both reps of CTCF, MYOD rep1


title: 15297X19 Abcb10 knockout cells Day 2 biol rep 4


title: H6-EGFP-3

description: Derived from sequence batch #1


title: B12-81


title: Input, RH30, for both reps of CTCF, MYOD rep1


title: H12-EGFP-2_batch2

description: Derived from sequence batch #2


title: 15297X18 Abcb10 knockout cells Day 2 biol rep 3


title: 15297X17 Abcb10 knockout cells Day 2 biol rep 2


title: H6-EGFP-2

description: Derived from sequence batch #1


title: B09-51


title: H6-EGFP-1

description: Derived from sequence batch #1


title: 15297X16 Abcb10 knockout cells Day 2 biol rep 1


title: Day_3_Lung_10^4_R3

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

data_processing:
Processing is automated using the RNAsik pipeline (https://doi.org/10.5281/zenodo.1403976). The workflow is as follows:
Reads are aligned using the STAR aligner (version 2.7.1b)
Aligned reads are sorted with Samtools (version 1.9) and marked duplicate with Picard (2.20.2)
Finally, reads assigned to features using featureCounts from SubRead (version 2.0.0)
Supplementary files format and content: Ensembl GRCh38
Supplementary files format and content: Tab delimited files including features ID's and feature information

source_name: H9 HES

growth_protocol: HES3 NKX2-5eGFP/w human embryonic stem cells were differentiated into mature cardiac cultures using the protocol described in the associated manuscript. H9 human embryonic stem cells were differentiated into type II alveolar lung cells using the protocol described in the associated manuscript.

extract_protocol:
RNA extraction was performed on the Qiacube (Qiagen) using the miRNeasy Micro Kit (#217084) and RNA quality was assessed using the Bioanalyser (Agilent RNA 6000 Pico kit).
The libraries were prepared using 0.5-2 ng of RNA samples. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. The Illumina P5 (5' AAT GAT ACG GCG ACC ACC GA 3') and P7 (5' CAA GCA GAA GAC GGC ATA CGA GAT 3') sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilizes a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification. Sequencing was performed on the NextSeq550 (Illumina), using the V2 High output kit (Illumina) in accordance with the Illumina Protocol 15046563 v02, generating 2 reads per cluster composed of a 19 bp R1 and a 72 bp R2.

treatment_protocol: Human stem cell-derived cardiac and lung cells grown in 24 well tissue culture plates were infected with 10^4 TCID50 of SARS-CoV-2. At 0-, 1-and 3-days post-infection, supernatant was removed, and the cell monolayer was lysed with 500μL of TRIzol reagent for RNA extraction.

value: H9 HES

value: Alveolar type II cell

value: 10^4 TCID50 SARS-CoV-2


title: Day_3_Lung_10^4_R2


title: 15297X15 WT MEL cells Day 2 biol rep 5

value: WT


title: H12-VPS45-3

description: Derived from sequence batch #1

value: VPS45 shRNA KD


title: F05-37

value: Kidney

value: Control

value: Xylose-free (0percent)


title: B08-82


title: B06-88


title: H12-VPS45-2

description: Derived from sequence batch #1

value: Glutamatergic, NGN2-induced, day-20 neuron


title: B04-87


title: H12-VPS45-1

description: Derived from sequence batch #1


title: Day_3_Lung_10^4_R1


title: Day_3_Lung_Mock_R3

value: Uninfected Control


title: 15297X13 WT MEL cells Day 2 biol rep 3


title: B01-50


title: H12-lncRNA-3

description: Derived from sequence batch #1

value: long non-coding RNA shRNA KD


title: Input, RH4, for both reps of CTCF, MYOD rep1 SEG0225


title: Day_3_Lung_Mock_R2


title: 15297X12 WT MEL cells Day 2 biol rep 2

value: MEL


title: 15297X11 WT MEL cells Day 2 biol rep 1


title: E11-23

source_name: Jejunum

value: Jejunum

value: Xylose treatment

value: 8percent D-xylose


title: E12-21


title: Day_3_Lung_Mock_R1


title: 15297X10 Abcb10 knockout cells Day 0 biol rep 5

value: Erythroleukemia cells

value: Abcb10 knockout

value: 0 days treatment


title: Day_1_Lung_10^4_R3

value: H9 HES

value: Alveolar type II cell


title: Day_1_Lung_10^4_R2

value: 10^4 TCID50 SARS-CoV-2


title: H12-EGFP-3

description: Derived from sequence batch #1

value: EGFP shRNA ctrl


title: Day_1_Lung_10^4_R1


title: H12-EGFP-2

description: Derived from sequence batch #1


title: E03-24


title: 15297X8 Abcb10 knockout cells Day 0 biol rep 3


title: H12-EGFP-1

description: Derived from sequence batch #1


title: 15297X14 WT MEL cells Day 2 biol rep 4

value: WT

value: 1.5% DMSO

value: 2 days treatment


title: 15297X7 Abcb10 knockout cells Day 0 biol rep 2


title: H12-C1orf54-3

description: Derived from sequence batch #1

value: Glutamatergic, NGN2-induced, day-20 neuron

value: C1orf54 shRNA KD


title: E01-25


title: H12-lncRNA-2

description: Derived from sequence batch #1

value: long non-coding RNA shRNA KD


title: Day_1_Lung_Mock_R2

value: Uninfected Control


title: 15297X6 Abcb10 knockout cells Day 0 biol rep 1

value: MEL


title: A11-11

value: Jejunum

value: Xylose treatment


title: H12-C1orf54-2

description: Derived from sequence batch #1


title: A10-124

value: 8percent D-xylose


title: H12-lncRNA-1

description: Derived from sequence batch #1


title: E09-29


title: Day_3_Cardiac_10^4_R2

source_name: HES3 NKX2-5eGFP/w

value: HES3 NKX2-5eGFP/w

value: Cardiac


title: Day_1_Lung_Mock_R1

value: H9 HES


title: A07-15


title: 15297X5 WT MEL cells Day 0 biol rep 5

value: Erythroleukemia cells

value: 0 days treatment


title: A11-VPS45-3

description: Derived from sequence batch #1

value: VPS45 shRNA KD


title: H12-C1orf54-1

description: Derived from sequence batch #1


title: 15297X4 WT MEL cells Day 0 biol rep 4

value: WT


title: Day_3_Cardiac_10^4_R1

value: 10^4 TCID50 SARS-CoV-2


title: 15297X9 Abcb10 knockout cells Day 0 biol rep 4

value: Abcb10 knockout


title: A05-18


title: E06-32


title: 15297X3 WT MEL cells Day 0 biol rep 3


title: Day_1_Lung_Mock_R3

value: Alveolar type II cell


title: A03-125


title: A11-VPS45-2

description: Derived from sequence batch #1

value: Glutamatergic, NGN2-induced, day-20 neuron


title: A11-VPS45-1

description: Derived from sequence batch #1


title: Day_3_Cardiac_Mock_R1


title: 15297X2 WT MEL cells Day 0 biol rep 2


title: 15297X1 WT MEL cells Day 0 biol rep 1


title: E10-28

value: Control

value: Xylose-free (0percent)


title: Day_1_Cardiac_10^4_R2


title: A11-lncRNA-3

description: Derived from sequence batch #1

value: long non-coding RNA shRNA KD


title: Huh7 cells, UBL5-siRNA3

city: Richmond

first: Xianjun

last: Fang

state: Virginia

address: 1101 E. Marshall Street, Sanger Hal, Sanger Hall, Room 2-016D

institute: Virginia Commonwealth university

data_processing:
Demultiplexing with Bcl2fastq2 was employed to generate the fastq file for each sample. The average of 30M reads were obtained for this set of samples.
The quality of RNA-Seq reads was assessed with FastQC v0.11.9.
The reads were aligned using STAR aligner version 2.7.6a to reference genome GRCh38.
Raw gene counts of mapped reads were aggregated using featureCounts.
The differential gene expression analysis was performed with Bioconductor package DESeq2 v1.30.0 using the normalized and filtered counts per gene from the RNA-Seq data.
Assembly: GRCh38
Supplementary files format and content: csv data after DESeq2 program include gene ID, count, log2foldchange, p-value, padj

growth_protocol: HepG2 and Huh7 cells were maintained in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared following the Illumina TruSeq stranded mRNA sample preparation guide.

treatment_protocol:
The cells were transfected with UBL5-siRNA or non-target Control-siRNA by lipofectamine RNAiMAX. The fresh medium was changed after overnight incubation.
The cells were kept in humidified atmosphere with 5% CO2 at 37C for another 36 hours.

value: hepatocellular carcinoma

value: UBL5 knockdown

value: siRNA

value: 52 hours


title: Huh7 cells, UBL5-siRNA2


title: A11-lncRNA-2

description: Derived from sequence batch #1


title: E08-30

value: Jejunum


title: Day_1_Cardiac_Mock_R2

value: HES3 NKX2-5eGFP/w

value: Cardiac

value: Uninfected Control


title: Day_1_Cardiac_10^4_R1


title: E07-22


title: Huh7 cells, Control-siRNA3


title: E05-31


title: A11-lncRNA-1

description: Derived from sequence batch #1


title: E04-26


title: Day_3_Cardiac_Mock_R2


title: E02-27


title: A11-EGFP-2

description: Derived from sequence batch #1

value: EGFP shRNA ctrl


title: Day_1_Cardiac_Mock_R1


title: Huh7 cells, Control-siRNA1

value: WT


title: A11-EGFP-1

description: Derived from sequence batch #1


title: A12-126


title: HepG2 cells, UBL5-siRNA3


title: Huh7 cells, Control-siRNA2


title: A11-EGFP-3

description: Derived from sequence batch #1


title: A11-lncRNA-4

description: Derived from sequence batch #1


title: A11-C1orf54-3

description: Derived from sequence batch #1

value: C1orf54 shRNA KD


title: A09-14


title: A02-13

value: Xylose treatment

value: 8percent D-xylose


title: A11-C1orf54-2

description: Derived from sequence batch #1

value: Glutamatergic, NGN2-induced, day-20 neuron


title: A08-123

value: Control


title: HepG2 cells, UBL5-siRNA2


title: Huh7 cells, UBL5-siRNA1


title: A11-C1orf54-1

description: Derived from sequence batch #1


title: A04-127

value: Xylose-free (0percent)


title: TGF-beta treated NHBE ALI 3

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Adapters were removed using Trimmomatic-0.39
Reads were aligned to hg19 genome using STAR v2.7.2
Gene expression was quantified using Cuffinks v2.2.1
The number of reads was summarized at the gene level using featureCounts v1.6.4
DESeq2 v1.24 was used to determine differential expression. Genes were considered to differentially expressed with a FDR < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: TGF-beta treated NHBE ALI

extract_protocol: RNA-Seq libraries were prepared using the NEBNext Ultra II nondirectional Ribodepletion kit

value: normal human bronchial epithelial (MHNE) cells

value: TGF-beta


title: HepG2 cells, Control-siRNA2

value: hepatocellular carcinoma


title: TGF-beta treated NHBE ALI 2


title: A06-128


title: HepG2 cells, Control-siRNA3

value: siRNA


title: A01-12


title: HepG2 cells, Control-siRNA1

value: 52 hours


title: TGF-beta treated NHBE ALI 1


title: ChIP_PAF1_1h_20E

status: Public on Jun 12 2023

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq reads were aligned to the dm6 genome using bowtie2 v2.2.9 with parameters -t -p 8 --local
Assembly: FB2017_02 Dmel Release 6.15
Supplementary files format and content: Wig files were generated using Spp v1.11 and converted to bigWig using wigToBigWig v4. Scores represent number of reads normalized by the size of the library.

organism: Drosophila melanogaster

source_name: S2 Schneider cells

growth_protocol: Drosophila Schneider line 2 (S2) cells were maintained at 25°C in the ecdysone-free Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 10 ?g of antibodies and 8 ?L of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 ?L per 500 ?L sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 ?L of proteinase K and 5 ?L of 0.5M EDTA per 500 ?L sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Mnase-ChIP seq was performed with the same protocol except one stage. Step of chromatin sonication was change to treatment with Micrococcal nuclease (ThermoScientific) for 5 min at 37°C and for 30 min at 4°C.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 0.3 µM 20-hydroxyecdysone (Sigma, http://www.sigmaaldrich.com/catalog/product/sigma/h5142) to induce the ecdysone cascade.

value: S2 Schneider cells

tag: time of 20h-ecdysone treatment

value: 1 hour

tag: 20h-ecdysone concentration

tag: chip antibody

value: Custom-made  (against 1-234 aa of PAF1) described in PMID:29410381


title: ChIP_MNase_H3K27Ac_0h_DMSO

value: sham-treated DMSO

value: 0 uM

value: Active motif antibodies against Histone H3K27Ac (39133)


title: ChIP_MNase_H3K27Ac_1h_20E


title: ChIP_Spt5_0h_DMSO

value: Custom-made  (against 917-1117 aa of Spt5) described in PMID:29410381


title: ChIP_Spt5_1h_20E


title: ChIP_PAF1_0h_DMSO


title: HepG2 cells, UBL5-siRNA1

value: UBL5 knockdown


title: ChIP_cdk8_0h_DMSO

value: Custom-made  (against 293-394 aa of cdk8) described in PMID:29410381


title: ChIP_dSet1_1h_20E

value: Custom-made  (against 1–103 aa of dSet1) described in PMID:29410381


title: ChIP_dSet1_0h_DMSO


title: ChIP_lid_0h_DMSO

value: Custom-made  (against 1–165 aa of lid/Kdm5) described in PMID:29410381


title: ChIP_cdk8_1h_20E


title: ChIP_Gcn5_1h_20E

value: Custom-made  (against 349–813 aa of Gcn5) described in PMID:23609539


title: ChIP_Gcn5_0h_DMSO

value: Custom-made  (against 349–813 aa of Gcn5) described in PMID:23609538


title: ChIP_DART1_1h_20E

value: Custom-made  (against 1-100 aa aa of DART1) described in PMID:29410381


title: ChIP_CHD1_0h_DMSO

value: Custom-made  (against 1420-1651 aa of CHD1) described in PMID:29410381


title: ChIP_CHD1_1h_20E


title: ChIP_DART1_0h_DMSO


title: ChIP_KisL_1h_20E

value: Custom-made  (against 1150-1314 aa of KisL) described in PMID:29410381


title: ChIP_KisL_0h_DMSO


title: ChIP_Brm_1h_20E

value: Custom-made (against 1513-1646 aa of Brm) described in PMID:29410381


title: endometrium, IUA patient, rep5

city: Nanjing

first: Simin

last: Yao

address: 321 Zhongshan Road

country: China

institute: The Affiliated Drum Tower Hosipital, Medical School, Nanjing University

description: Ba5 from IUA patient 5

data_processing:
Illumina Casava1.7 software used for basecalling.
We used fastp for quality control of raw reads, filtered low quality data, and obtained clean reads.
Reference genome-based alignment analysis was performed with the use of HISAT2 software.
Based on the HISAT2 alignment results, we reconstructed transcripts using Stringtie and calculated the expression of all genes in each sample using RSEM.
To identify differentially expressed mRNAs across samples or groups, the DESeq2 package (http://www.bioconductor.org/) was used. We identified mRNAs with a fold change ≥2 and a P value <0.05 in a comparison between samples or groups as significant differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: endometrium

extract_protocol:
Endometria were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#RS-200-0048) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: endometrium

tag: disease state

value: IUA patient


title: endometrium, IUA patient, rep6

description: Ba6 from IUA patient 6


title: endometrium, IUA patient, rep7

description: Ba7 from IUA patient 7


title: endometrium, IUA patient, rep4

description: Ba4 from IUA patient 4


title: ChIP_lid_1h_20E

value: S2 Schneider cells

value: 1 hour


title: endometrium, IUA patient, rep3

description: Ba3 from IUA patient 3


title: endometrium, IUA patient, rep1

description: Ba1 from IUA patient 1


title: endometrium, IUA patient, rep2

description: Ba2 from IUA patient 2


title: endometrium, normal control, rep5

description: Con5 from normal control 5

value: normal control


title: endometrium, normal control, rep2

description: Con2 from normal control 2


title: endometrium, normal control, rep4

description: Con4 from normal control 4


title: endometrium, normal control, rep6

description: Con6 from normal control 6


title: endometrium, normal control, rep7

description: Con7 from normal control 7


title: endometrium, normal control, rep1

description: Con1 from normal control 1


title: endometrium, normal control, rep3

description: Con3 from normal control 3


title: Blood_Platelets_Vumc-NSCLC-140

city: Amsterdam

first: Mafalda

last: Antunnes

state: zuid holland

address: de boelelaan 1118

department: NRG

country: Netherlands

institute: Amsterdam UMC

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Assembly: hg19
Supplementary files format and content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

source_name: Thrombocytes

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

value: Thrombocytes

tag: cancer stage

tag: patient group

value: NSCLC


title: Blood_Platelets_Vumc-NSCLC-143

tag: cell type


title: Blood_Platelets_Vumc-NSCLC-139


title: Blood_Platelets_Vumc-NSCLC-150


title: Blood_Platelets_Vumc-NSCLC-142


title: Blood_Platelets_Vumc-NSCLC-144


title: Blood_Platelets_Vumc-NSCLC-138


title: Blood_Platelets_Vumc-NSCLC-154


title: Blood_Platelets_Vumc-NSCLC-136


title: Blood_Platelets_Vumc-NSCLC-114


title: Blood_Platelets_Vumc-NSCLC-132-1


title: Blood_Platelets_Vumc-NSCLC-125


title: Blood_Platelets_Vumc-NSCLC-134


title: Blood_Platelets_Vumc-NSCLC-122


title: Blood_Platelets_Vumc-NSCLC-109-1


title: Blood_Platelets_Vumc-NSCLC-089


title: Blood_Platelets_Vumc-NSCLC-113


title: Blood_Platelets_Vumc-NSCLC-084


title: Blood_Platelets_Vumc-NSCLC-086


title: Blood_Platelets_Vumc-NSCLC-080


title: ChIP_Brm_0h_DMSO

value: sham-treated DMSO

value: 0 uM

value: Custom-made (against 1513-1646 aa of Brm) described in PMID:29410380


title: E39 ferret cortex 1

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

description:
Wild type ferret cortex
E39.csv

data_processing:
cellranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting.
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data.
Finally, Seurat (V3) were used for the following dimensionality reduction, clustering, and gene expression.
Assembly: mm10 for mice and ASM1176430v1.1 for Ferret
Supplementary files format and content: gene count

organism: Mustela putorius furo

source_name: E39 ferret cortex

extract_protocol:
The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C).
The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions.

treatment_protocol: For mouse cortex: E18 wild type and Smo CKO (Flash-Tag were injected at E17, and the cortex was harvested at E18) cortices were carefully dissected under a fluorescent stereoscope, and incubated in 4 ml of papain solution for 20 min at 37℃, The cortical tissues were gently triturated, filtered through a 40 mm strainer, and washed with HBSS to obtain the single cell suspension. The wild type E39 ferret cortex were dissected and the treatment methods are the same as those of mice.

value: Cortex

tag: developmental stage

value: Embryonic day 39


title: Blood_Platelets_Vumc-NSCLC-063


title: Blood_Platelets_Vumc-NSCLC-133


title: E39 ferret cortex 2

description:
Wild type ferret cortex
E39.csv


title: Blood_Platelets_Vumc-HC-0069-TR2666

value: Control


title: Blood_Platelets_VUMC-HC-0053-TR3025


title: Blood_Platelets_Vumc-HC-0161-TR2606


title: Participant 19, timepoint 16

city: Durham

first: Robert

last: Moseley

address: 124 Science Drive

institute: Duke University

description: ex vivo whole blood

data_processing:
Each participant's set of Fastq files were aligned to human and parasite genome reference files using STAR (version 2.7.5c)  and quantified using RSEM (version 1.3.3)
PlasmoDB-50_PvivaxP01.gff was first converted to a .gtf file using the new code scripts created for this study (see Key resources table of the manuscript)
The STAR command used for building the human STAR index was STAR --runThreadN <int> --runMode genomeGenerate --genomeDir <output_directory> --genomeFastaFiles <reference_sequence_file> --sjdbGTFfile <annotation_file>
The command for building the parasite STAR index was STAR --runThreadN <int> --runMode genomeGenerate --genomeSAindexNbases 11 --genomeDir <output_directory> --genomeFastaFiles <reference_sequence_file> --sjdbGTFfile <annotation_file>
The RSEM command, which was run once for each organism, used for building the human and parasite RSEM index was rsem-prepare-reference --num-threads <int> --gtf <annotation_file> <reference_sequence_file> <output_directory>
The STAR command for aligning reads from a single Fastq file to the human genome was STAR --runThreadN <int> --runMode alignReads --genomeDir <human_STAR_index> --readFilesIn <Fastq_file> --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --readFilesCommand zcat --outFilterType BySJout --outFileNamePrefix <output_directory> --outFilterIntronMotifs RemoveNoncanonical
The STAR command for aligning reads from a single Fastq file to the parasite genome was STAR --runThreadN <int> --runMode alignReads --genomeDir <parasite_STAR_index> --readFilesIn <Fastq_file> --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --readFilesCommand zcat --outFilterType BySJout --alignIntronMin 10 --alignIntronMax 3000 --outFileNamePrefix <output_directory> --outFilterIntronMotifs RemoveNoncanonical
Reads from a single Fastq file could map to both organisms' genomes, which can result in inaccurate quantification results. To remove the small number of reads that map to both organisms' genomes, we identified reads that were present in both the human- and parasite-associated BAM files generated from aligning a single Fastq file using STAR. These reads were then removed from both BAM files, producing new human- and parasite-associated BAM files that contained reads uniquely mapped to the respective organism. These new BAM files were used in the quantification step.
The RSEM command for quantification of the reads uniquely aligned to the human genome was rsem-calculate-expression -p <int> --bam --strandedness reverse --fragment-length-mean <avg_fragment_length> --fragment-length-sd <fragment_lenght_std_dev> --no-bam-output <filtered_BAM_file> <human_RSEM_index> <output_directory>
The RSEM command for quantification of the reads uniquely aligned to the parasite genome was rsem-calculate-expression -p <int> --strandedness reverse --fragment-length-mean <avg_fragment_length> --fragment-length-sd <fragment_lenght_std_dev> --bam --no-bam-output <filtered_BAM_file> <parasite_RSEM_index> <output_directory>
Alignment and quantification was performed on the Duke Compute Cluster (https://rc.duke.edu/dcc/) at Duke University which, at the time of use, used CentOS 8 as the operating system and SLURM as the scheduler for the entire system.
Genes which appear in the comprehensive gene annotation file but which were not expressed (i.e. 0 TPM units) at any time point by a participant or parasite population were removed.
Within the GENCODE comprehensive gene annotation file used for this study are 44 genes with duplicate copies in the pseudoautosomal regions on the X and Y chromosomes (Table S2 of manuscript). Since each of these 44 pairs contained two copies of the same gene, quantification resulted in 44 pairs of duplicated expression profiles for each study participant. Because each participant is male, we added together the duplicate expression profiles in the 44 pairs and retained only a single copy of the duplicated genes. In this way we ensured that pseudoautosomal genes could not have an outsized influence in downstream analyses (e.g. circadian phase estimates) if these genes were found to be highly periodic and sufficiently highly expressed.
QuIn this study, species-specific Quantile Normalization was independently applied to each participant's samples and each participant's parasite samples. In particular, genes within each sample (participant, organism, and time point) were sorted according to their TPM values, thereby ranking genes from least expressed to most expressed in each organism and time point. The average TPM value of all genes occupying the same rank in these sorted lists was then computed across all timepoints within each participant and organism and the original TPM value of each gene was replaced with the average of all genes occupying it's same rank. Here care was taken to include all equally-ranked genes, including those which are ambiguously ranked because they have identical TPM values within a sample. Finally, each sample was reordered by gene, to realign the now between-sample normalized expression levels.
Sample 18's hour-24 time point sample was accidentally destroyed prior to RNA sequencing. Expression levels for this time point were interpolated following Quantile Normalization using Piecewise Cubic Hermite Interpolating Polynomial (PCHIP) interpolation.
Assembly: human: gencode.GRCh38.primary_assembly.genome.fa ; parasite: PlasmoDB-50_PvivaxP01_Genome.fasta
genome feature file: human: gencode.v36.primary_assembly.annotation.gtf; parasite: PlasmoDB-50_PvivaxP01.gff
Supplementary files format and content: Each Sample, e.g., Sample 02, has a tab-delimited text file containing quantile normalized TPM values for each sampling time point.
Supplementary files format and content: counts_human.tsv and counts_vivax.tsv files contain the expected read counts as determined by RSEM for each gene.

organism:
Plasmodium vivax
Homo sapiens

source_name: whole blood

growth_protocol: 18 ml of blood was drawn from each study participant into heparin tubes for the ex vivo time series experiment. 3.2 ml of the sample was mixed with 156.8 ml of McCoy’s 5A culture media supplemented with 2 mM of L-glutamine, 20% AB serum, generating a 2% haematocrit sample. To collect the culture sample at 3 hour intervals over the subsequent 48 hours, 10 ml of the culture mixture were aliquotted into 25 cm2 culture flasks (16 flasks in total for each study participant). Cultures were gassed with 5% CO2, 5% O2, 90% N2 gas and placed in an incubator at 37°C. Approximately every 3 hours, one of the culture flasks was removed, and media and cell pellets were kept in separate tubes and placed immediately in liquid nitrogen, for a total of 17 time point samples including the time 0 sample.

extract_protocol:
Frozen cell pellets were used for RNA extraction using the Agencourt RNAdvance Blood RNA purification kit and associated protocols. Samples were cleaned before sequencing with Zymo Research OneStepTM PCR Inhibitor Removal Kit.
Libraries were constructed using a kit specific for blood that depleted both ribosomal and globin RNAs.

value: whole blood

value: Plasmodium vivax infected

value: hr 45

tag: study participant


title: Blood_Platelets_Vumc-HC-0140-TR2602


title: Blood_Platelets_Vumc-NSCLC-083


title: Blood_Platelets_Vumc-HC-0068-TR2665


title: Participant 19, timepoint 13

description: ex vivo whole blood

tag: tissue

value: hr 36


title: Blood_Platelets_Vumc-HC-0131-TR2600


title: Participant 19, timepoint 11

description: ex vivo whole blood

value: hr 30


title: Participant 19, timepoint 8

description: ex vivo whole blood

value: hr 21


title: Participant 19, timepoint 12

description: ex vivo whole blood

value: hr 33


title: Blood_Platelets_Vumc-HC-0125-TR2436


title: Participant 19, timepoint 10

description: ex vivo whole blood

value: hr 27


title: Blood_Platelets_Vumc-HC-0103-TR2435


title: Blood_Platelets_Vumc-HC-0129-TR2437


title: Participant 19, timepoint 9

description: ex vivo whole blood

value: hr 24


title: Blood_Platelets_Vumc-HC-0084-TR2434

value: Thrombocytes


title: Participant 19, timepoint 6

description: ex vivo whole blood

value: hr 15


title: Participant 19, timepoint 7

description: ex vivo whole blood

value: hr 18


title: Blood_Platelets_Vumc-HC-0143-TR2404


title: Blood_Platelets_Vumc-HC-0083-TR2403


title: Participant 19, timepoint 15

description: ex vivo whole blood

value: hr 42


title: Participant 19, timepoint 4

description: ex vivo whole blood

value: hr 9


title: Participant 19, timepoint 5

description: ex vivo whole blood

value: hr 12


title: Blood_Platelets_Vumc-HC-0151-TR2605


title: Blood_Platelets_Vumc-HD-283-2-TR1875


title: Participant 19, timepoint 14

description: ex vivo whole blood

value: hr 39


title: Blood_Platelets_Vumc-HC-0094-TR2594

value: Control


title: Blood_Platelets_Vumc-HD-245-TR1858


title: Participant 19, timepoint 2

description: ex vivo whole blood

value: whole blood

value: hr 3


title: Participant 19, timepoint 3

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 6


title: Blood_Platelets_Vumc-HD-282-2-TR1873


title: Blood_Platelets_NKI-NSCLC-1470-TR1384

value: NSCLC


title: Participant 18, timepoint 15

description: ex vivo whole blood


title: Blood_Platelets_NKI-NSCLC-1362-TR1381


title: Participant 18, timepoint 14

description: ex vivo whole blood


title: Blood_Platelets_Vumc-HD-34-2-TR1490


title: Blood_Platelets_NKI-NSCLC-1652-TR1344


title: Participant 18, timepoint 13

description: ex vivo whole blood

value: hr 36


title: Blood_Platelets_NKI-NSCLC-1459-TR1339


title: Blood_Platelets_NKI-NSCLC-1476-TR1342


title: Blood_Platelets_NKI-NSCLC-1420-TR1338


title: Participant 19, timepoint 1

description: ex vivo whole blood

value: hr 0


title: Participant 18, timepoint 11

description: ex vivo whole blood

value: hr 30


title: Participant 18, timepoint 8

description: ex vivo whole blood

value: hr 21


title: Participant 18, timepoint 16

description: ex vivo whole blood

value: hr 45


title: Participant 18, timepoint 12

description: ex vivo whole blood

value: hr 33


title: Blood_Platelets_NKI-NSCLC-1565-TR1345

value: Thrombocytes


title: Participant 18, timepoint 10

description: ex vivo whole blood

value: hr 27


title: Participant 18, timepoint 7

description: ex vivo whole blood

value: hr 18


title: Blood_Platelets_NKI-NSCLC-1342-TR1334


title: Participant 18, timepoint 5

description: ex vivo whole blood

value: hr 12


title: Blood_Platelets_NKI-NSCLC-1349-TR1333


title: Blood_Platelets_NKI-NSCLC-1613-TR1335


title: Participant 18, timepoint 4

description: ex vivo whole blood

value: hr 9


title: Blood_Platelets_NKI-NSCLC-1029-TR1328


title: Participant 18, timepoint 3

description: ex vivo whole blood


title: Blood_Platelets_NKI-NSCLC-1059-TR1327


title: Participant 18, timepoint 2

description: ex vivo whole blood


title: Participant 17, timepoint 16

description: ex vivo whole blood


title: Participant 18, timepoint 1

description: ex vivo whole blood


title: Blood_Platelets_NKI-NSCLC-882-TR1319


title: Blood_Platelets_NKI-NSCLC-1422-TR1337


title: Blood_Platelets_NKI-NSCLC-1198-TR1318


title: Blood_Platelets_NKI-NSCLC-1409-TR1336


title: Blood_Platelets_NKI-NSCLC-975-TR1317


title: Blood_Platelets_NKI-NSCLC-1369-TR1311


title: Blood_Platelets_NKI-NSCLC-1082-TR1322


title: Participant 17, timepoint 15

description: ex vivo whole blood

value: hr 42


title: Participant 17, timepoint 14

description: ex vivo whole blood

value: whole blood

value: hr 39


title: Participant 17, timepoint 13

description: ex vivo whole blood

value: Plasmodium vivax infected


title: Participant 17, timepoint 10

description: ex vivo whole blood


title: Blood_Platelets_Vumc-NSCLC-574-TR1307


title: Participant 17, timepoint 11

description: ex vivo whole blood


title: Blood_Platelets_NKI-NSCLC-1379-TR1309


title: Participant 17, timepoint 12

description: ex vivo whole blood


title: Participant 18, timepoint 6

description: ex vivo whole blood

value: hr 15


title: Participant 17, timepoint 9

description: ex vivo whole blood

value: hr 24


title: Blood_Platelets_Vumc-NSCLC-514-TR1306

value: NSCLC


title: Blood_Platelets_Vumc-NSCLC-574-TR1307-seq2


title: Participant 17, timepoint 7

description: ex vivo whole blood


title: Blood_Platelets_Vumc-NSCLC-513-TR1305


title: Participant 17, timepoint 8

description: ex vivo whole blood


title: Participant 17, timepoint 6

description: ex vivo whole blood


title: Blood_Platelets_Vumc-NSCLC-461-TR1303


title: Participant 17, timepoint 5

description: ex vivo whole blood


title: Blood_Platelets_Vumc-NSCLC-335-TR1294


title: Blood_Platelets_NKI-NSCLC-865-TR1312


title: Blood_Platelets_NKI-NSCLC-1535-TR1308


title: Participant 17, timepoint 4

description: ex vivo whole blood


title: Participant 17, timepoint 3

description: ex vivo whole blood

value: hr 6


title: Blood_Platelets_Vumc-NSCLC-251-TR1276


title: Blood_Platelets_Vumc-NSCLC-394-TR1273


title: Participant 17, timepoint 2

description: ex vivo whole blood

value: hr 3


title: Participant 16, timepoint 14

description: ex vivo whole blood


title: Participant 16, timepoint 16

description: ex vivo whole blood


title: Participant 17, timepoint 1

description: ex vivo whole blood

value: hr 0


title: Blood_Platelets_NKI-NSCLC-1128-TR1285


title: Blood_Platelets_NKI-NSCLC-1143-TR1282


title: Blood_Platelets_Vumc-NSCLC-288-TR1268


title: Blood_Platelets_Vumc-NSCLC-470-TR1275


title: Blood_Platelets_Vumc-NSCLC-391-TR1272


title: Participant 16, timepoint 13

description: ex vivo whole blood

value: hr 36


title: Participant 16, timepoint 15

description: ex vivo whole blood


title: Participant 16, timepoint 11

description: ex vivo whole blood

value: hr 30


title: Participant 16, timepoint 10

description: ex vivo whole blood


title: Blood_Platelets_Vumc-NSCLC-323-TR1245

value: Thrombocytes


title: Blood_Platelets_Vumc-NSCLC-313-TR1243


title: Blood_Platelets_Vumc-NSCLC-258-TR1238


title: Blood_Platelets_Vumc-NSCLC-178-TR1255


title: Participant 16, timepoint 8

description: ex vivo whole blood

value: hr 21


title: Blood_Platelets_Vumc-NSCLC-253-TR1237


title: Participant 16, timepoint 7

description: ex vivo whole blood

value: hr 18


title: Blood_Platelets_Vumc-NSCLC-317-TR1244


title: Participant 16, timepoint 9

description: ex vivo whole blood


title: Blood_Platelets_Vumc-NSCLC-300-TR1034


title: Participant 16, timepoint 6

description: ex vivo whole blood


title: Blood_Platelets_Vumc-NSCLC-296-TR1032


title: TCR_VILI_2

city: Basel

first: Sarp

last: Uzun

address: Schönbeinstrasse 40

country: Switzerland

institute: University Hospital Basel, Institute of Medical Genetics and Pathology

data_processing:
UBAM files were uploaded to Ion Reporter Software, Version 5.18 (ThermoFisher).
Oncomine TCR Beta-SR - w1.4 - RNA and Oncomine BCR IGH-SR - w1.4 - RNA workflows were used for read alignment to IMGT database of variable, diversity and joining genes.
T- and B-cell clone CDR3 sequence, variable and joining gene information was generated by the Ion Reporter Software
Assembly: IMGT® database of variable, diversity and joining genes as a reference
Supplementary files format and content: Excel files contaning read count per T-cell clone, variable gene, joining gene, CDR3 nucleotide sequence, CDR3 amino acid sequence
Supplementary files format and content: Excel files contaning read count per B-cell clone, variable gene, joining gene, CDR3 nucleotide sequence, CDR3 amino acid sequence
Library strategy: TCR-seq

extract_protocol:
25-30 μm thick FFPE tissue sections were obtained from each patient, deparaffinized with xylene, and total RNA and DNA were extracted simultaneously with the AllPrep DNA/RNA FFPE Kit (Qiagen, 80234) following the vendor's instructions. Final DNA and RNA concentrations were measured with Qubit dsDNA HS Assay Kit (ThermoFisher, Q32851) and RNA HS Assay Kits (ThermoFisher, Q32852), respectively. RNA isolated from PaxGene storted frozen blood sample of VILI_5 with PAXgene Blood RNA Kit according to vendor's protocol. Total RNA isolation from T-cells performed with Allprep DNA/RNA Mini Kit according to vendor's protocol.
cDNA was synthesized from RNA by using the SuperScript VILO cDNA Synthesis Kit (Invitrogen, 11754250) and Ion Torrent NGS Reverse Transcription Kit (ThermoFisher, A45003) for TCR and BCR sequencing, respectively. T-cell and B-cell RNA was quantified by qPCR with TaqMan Gene Expression Assay, CD247 (20X, Hs00167901_m1) and CD19 (20X, Hs01047413_g1). Final input was normalized to 1 ng of T- and B-cell derived RNA per sample. For samples with low T- and B-cell counts, maximum RNA input was loaded for library preparation. Next-Generation Sequencing (NGS) libraries were prepared using the Oncomine TCR Beta-SR RNA Assay (ThermoFisher, A39359) and the Oncomine BCR IGH SR RNA Assay (ThermoFisher, A45484) according to manufacturer’s instructions. Amplified and barcode ligated libraries were purified with AMPure XP Reagent (Beckman Coulter, A63880) and quantified with the Ion Universal Library Quantitation Kit (ThermoFisher, A26217). The library pool was prepared by combining equal volumes of libraries at 50 pmol/L concentration and loaded into Ion 550™ Chip (ThermoFisher, A34537).

tag: cohort

value: Vaccine

tag: label


title: Participant 16, timepoint 4

description: ex vivo whole blood

value: hr 9


title: Blood_Platelets_Vumc-NSCLC-298-TR1033


title: Blood_Platelets_Vumc-NSCLC-282-TR1031


title: TCR_VILI_4


title: TCR_VILI_3


title: BCR_AIH_3

description: geo_submission_BCR_main_cohort_clones.xlsx

data_processing:
UBAM files were uploaded to Ion Reporter Software, Version 5.18 (ThermoFisher).
Oncomine TCR Beta-SR - w1.4 - RNA and Oncomine BCR IGH-SR - w1.4 - RNA workflows were used for read alignment to IMGT database of variable, diversity and joining genes.
T- and B-cell clone CDR3 sequence, variable and joining gene information was generated by the Ion Reporter Software
Assembly: IMGT® database of variable, diversity and joining genes as a reference
Supplementary files format and content: Excel files contaning read count per T-cell clone, variable gene, joining gene, CDR3 nucleotide sequence, CDR3 amino acid sequence
Supplementary files format and content: Excel files contaning read count per B-cell clone, variable gene, joining gene, CDR3 nucleotide sequence, CDR3 amino acid sequence
Library strategy: BCR-seq

source_name: Liver

value: Liver

value: Autoimmune

value: Patient 9


title: Participant 16, timepoint 3

description: ex vivo whole blood

value: whole blood

value: Plasmodium vivax infected


title: Blood_Platelets_Vumc-NSCLC-348-TR1035


title: TCR_Frei_WH


title: Participant 16, timepoint 12

description: ex vivo whole blood

value: hr 33


title: BCR_SR_26

value: Patient 8


title: Blood_Platelets_Vumc-NSCLC-269-TR1021

value: NSCLC


title: BCR_AIH_2

value: Patient 7


title: Participant 16, timepoint 1

description: ex vivo whole blood

value: hr 0


title: Blood_Platelets_Vumc-NSCLC-257-TR1234


title: BCR_AIH_1

value: Patient 6


title: Blood_Platelets_Vumc-NSCLC-267-TR1020


title: BCR_SR_30

value: Patient 5


title: Participant 13, timepoint 16

description: ex vivo whole blood

value: hr 45


title: Blood_Platelets_Vumc-NSCLC-265-TR1019

value: Thrombocytes


title: Participant 13, timepoint 15

description: ex vivo whole blood

value: hr 42


title: BCR_SR_29

value: Patient 4


title: BCR_SR_28

value: Patient 3


title: Participant 16, timepoint 2

description: ex vivo whole blood

value: hr 3


title: TCR_VILI_1

source_name: Blood

value: Blood

value: Vaccine


title: Participant 13, timepoint 14

description: ex vivo whole blood

value: whole blood

value: hr 39


title: BCR_SR_27

value: Liver

value: Autoimmune

value: Patient 2


title: Blood_Platelets_Vumc-NSCLC-260-TR1008

value: NSCLC


title: BCR_SR_25

value: Patient 1


title: BCR_SR_14


title: Participant 13, timepoint 13

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 36


title: Participant 13, timepoint 11

description: ex vivo whole blood

value: hr 30


title: BCR_SR_12


title: BCR_SR_11


title: Blood_Platelets_Vumc-NSCLC-250-TR1005

value: Thrombocytes


title: Participant 13, timepoint 12

description: ex vivo whole blood

value: hr 33


title: BCR_SR_10


title: BCR_SR_7


title: TCR_SR_AIH9

description: geo_submission_TCR_main_cohort_clones.xlsx

value: Patient 9


title: Blood_Platelets_Vumc-NSCLC-248-TR1004


title: Participant 13, timepoint 10

description: ex vivo whole blood

value: hr 27


title: Blood_Platelets_Vumc-NSCLC-243-TR1002


title: TCR_SR_AIH_6

value: Patient 5


title: Participant 13, timepoint 9

description: ex vivo whole blood

value: hr 24


title: TCR_SR_AIH_3


title: Blood_Platelets_Vumc-NSCLC-242-TR1001


title: TCR_AIH5-2

value: Patient 4


title: TCR_SR_AIH_4

value: Patient 3


title: Blood_Platelets_Vumc-NSCLC-241-TR1000


title: TCR_AIH1-2


title: BCR_SR_15

value: Vaccine

value: Patient 6


title: Blood_Platelets_Vumc-NSCLC-259-TR1007


title: Participant 13, timepoint 7

description: ex vivo whole blood

value: whole blood

value: hr 18


title: TCR_Vac8

value: Liver


title: Blood_Platelets_Vumc-NSCLC-240-TR999

value: NSCLC


title: TCR_SR_Vac5


title: TCR_SR_Vac7


title: Blood_Platelets_Vumc-NSCLC-232-TR998


title: TCR_SR_Vac4


title: TCR_SR_Vac0

value: Patient 2


title: Participant 13, timepoint 5

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 12


title: Blood_Platelets_Vumc-NSCLC-226-TR997

value: Thrombocytes


title: Participant 13, timepoint 4

description: ex vivo whole blood

value: hr 9


title: Participant 13, timepoint 3

description: ex vivo whole blood

value: hr 6


title: metabo_KO_07

city: Suita

first: Yuta

last: Tachibana

state: Osaka

address: 3-1, Yamadaoka

department: Research Institute for Microbial Diseases (RIMD)

institute: Osaka University

data_processing:
The gRNA sequencing reads were aligned to the gRNA library. The abundance of each gRNA was calculated and normalized to the total number of aligned reads.
Assembly: metabolism sublibrary for CRISPR screen
Supplementary files format and content: text file for each gRNA expresssion

organism: Toxoplasma gondii

source_name: RH

extract_protocol:
Toxoplasma genomic DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen).
Integrated gRNA sequences were amplified and barcoded by PCR with KOD FX Neo (TOYOBO). Genomic DNA (1μg) was used for the template. The resulting libraries were sequenced on a DNBSEQ-G400RS (MGI).

value: RH

value: tachyzoite


title: metabo_KO_05


title: metabo_KO_06


title: Blood_Platelets_Vumc-NSCLC-223-TR996


title: metabo_KO_04


title: metabo_KO_03


title: Participant 13, timepoint 2

description: ex vivo whole blood

value: hr 3


title: metabo_KO_02


title: Participant 13, timepoint 8

description: ex vivo whole blood

value: hr 21


title: Participant 13, timepoint 6

description: ex vivo whole blood

value: hr 15


title: Participant 13, timepoint 1

description: ex vivo whole blood

value: hr 0


title: metabo_KO_01


title: metabo_WT_08


title: Participant 11, timepoint 16

description: ex vivo whole blood

value: hr 45


title: metabo_WT_07


title: Blood_Platelets_Vumc-NSCLC-201-TR979


title: metabo_WT_05


title: Participant 11, timepoint 15

description: ex vivo whole blood

value: whole blood

value: hr 42


title: Blood_Platelets_Vumc-NSCLC-200-TR978


title: metabo_WT_03


title: metabo_WT_04


title: Participant 11, timepoint 14

description: ex vivo whole blood

value: hr 39


title: Blood_Platelets_Vumc-NSCLC-199-TR977

value: NSCLC


title: Blood_Platelets_Vumc-NSCLC-221-TR984


title: metabo_WT_02


title: Participant 11, timepoint 13

description: ex vivo whole blood

value: hr 36


title: Participant 11, timepoint 12

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 33


title: metabo_WT_01


title: metabo_P4


title: Blood_Platelets_Vumc-NSCLC-203-TR980

value: Thrombocytes


title: Blood_Platelets_Vumc-NSCLC-198-TR976


title: Blood_Platelets_Vumc-NSCLC-187-TR975


title: metabo_library


title: TCR_SR_Vac3

value: Liver

value: Vaccine

value: Patient 1


title: Participant 11, timepoint 11

description: ex vivo whole blood

value: hr 30


title: mem_nuc_KO_09

data_processing:
The gRNA sequencing reads were aligned to the gRNA library. The abundance of each gRNA was calculated and normalized to the total number of aligned reads.
Assembly: endomembrane-nucleus sublibrary for CRISPR screen
Supplementary files format and content: text file for each gRNA expresssion

value: RH

value: tachyzoite


title: mem_nuc_KO_08


title: Participant 11, timepoint 10

description: ex vivo whole blood

value: hr 27


title: mem_nuc_KO_10


title: metabo_WT_06


title: mem_nuc_KO_06


title: Blood_Platelets_Vumc-NSCLC-171-TR962


title: mem_nuc_KO_07


title: Participant 11, timepoint 9

description: ex vivo whole blood

value: hr 24


title: mem_nuc_KO_04


title: Participant 11, timepoint 8

description: ex vivo whole blood

value: hr 21


title: Blood_Platelets_Vumc-NSCLC-159-TR957


title: Blood_Platelets_Vumc-NSCLC-149-TR954-seq2


title: mem_nuc_KO_03


title: mem_nuc_KO_02


title: Participant 11, timepoint 7

description: ex vivo whole blood

value: whole blood

value: hr 18


title: mem_nuc_KO_01


title: mem_nuc_WT_29


title: Blood_Platelets_Vumc-NSCLC-149-TR954


title: Blood_Platelets_Vumc-NSCLC-186-TR974


title: Blood_Platelets_Vumc-NSCLC-148-TR953


title: mem_nuc_WT_28


title: Participant 11, timepoint 5

description: ex vivo whole blood

value: hr 12


title: Blood_Platelets_Vumc-NSCLC-163-TR959

value: NSCLC


title: mem_nuc_WT_27


title: mem_nuc_WT_26


title: Blood_Platelets_Vumc-NSCLC-239-TR940


title: mem_nuc_WT_25


title: mem_nuc_WT_23


title: mem_nuc_WT_24


title: Blood_Platelets_Vumc-NSCLC-236-TR939


title: mem_nuc_WT_22


title: mem_nuc_KO_05


title: Participant 11, timepoint 3

description: ex vivo whole blood

value: hr 6


title: Participant 11, timepoint 4

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 9


title: Blood_Platelets_Vumc-NSCLC-219-TR916

value: Thrombocytes


title: Participant 11, timepoint 2

description: ex vivo whole blood

value: hr 3


title: mem_nuc_WT_21


title: mem_nuc_WT_18


title: mem_nuc_WT_17


title: Blood_Platelets_Vumc-NSCLC-225-TR905


title: mem_nuc_WT_16


title: Participant 11, timepoint 6

description: ex vivo whole blood

value: hr 15


title: Participant 10, timepoint 16

description: ex vivo whole blood

value: hr 45


title: mem_nuc_WT_15


title: Blood_Platelets_Vumc-NSCLC-217-TR904


title: Blood_Platelets_Vumc-NSCLC-208-TR902


title: mem_nuc_WT_13


title: Participant 10, timepoint 15

description: ex vivo whole blood

value: hr 42


title: Blood_Platelets_Vumc-NSCLC-204-TR901


title: mem_nuc_P4_3

value: RH


title: Participant 10, timepoint 14

description: ex vivo whole blood

value: hr 39


title: mem_nuc_WT_11

value: tachyzoite


title: mem_nuc_P4_1


title: mem_nuc_WT_12


title: Blood_Platelets_Vumc-NSCLC-194-TR899


title: Blood_Platelets_Vumc-NSCLC-191-TR898


title: Participant 10, timepoint 13

description: ex vivo whole blood

value: hr 36


title: mem_nuc_library


title: Participant 10, timepoint 12

description: ex vivo whole blood

value: hr 33


title: mem_nuc_P4_2


title: Participant 16, timepoint 5

description: ex vivo whole blood

value: whole blood


title: Participant 11, timepoint 1

description: ex vivo whole blood

value: hr 0


title: Blood_Platelets_Vumc-NSCLC-230-TR882


title: Participant 10, timepoint 11

description: ex vivo whole blood

value: hr 30


title: mem_nuc_WT_14


title: Participant 10, timepoint 10

description: ex vivo whole blood

value: hr 27


title: ROP_GRA_KO_07

data_processing:
The gRNA sequencing reads were aligned to the gRNA library. The abundance of each gRNA was calculated and normalized to the total number of aligned reads.
Assembly: ROP/GRA sublibrary for CRISPR screen
Supplementary files format and content: text file for each gRNA expresssion


title: ROP_GRA_KO_06


title: ROP_GRA_KO_05


title: ROP_GRA_KO_04


title: Blood_Platelets_Vumc-NSCLC-229-TR881

value: NSCLC


title: ROP_GRA_KO_03


title: ROP_GRA_KO_02


title: Participant 10, timepoint 9

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 24


title: Blood_Platelets_Vumc-NSCLC-224-TR879

value: Thrombocytes


title: Blood_Platelets_Vumc-NSCLC-212-TR878


title: ROP_GRA_WT_36


title: Blood_Platelets_Vumc-NSCLC-195-TR877


title: Participant 10, timepoint 8

description: ex vivo whole blood

value: hr 21


title: ROP_GRA_WT_35


title: ROP_GRA_KO_01


title: ROP_GRA_WT_28


title: Blood_Platelets_Vumc-NSCLC-181-TR876


title: ROP_GRA_WT_34


title: Participant 10, timepoint 7

description: ex vivo whole blood

value: hr 18


title: ROP_GRA_WT_27


title: Blood_Platelets_Vumc-NSCLC-213-TR872


title: ROP_GRA_WT_26


title: Participant 10, timepoint 5

description: ex vivo whole blood

value: hr 12


title: ROP_GRA_WT_32


title: ROP_GRA_WT_25


title: Blood_Platelets_Vumc-NSCLC-209-TR871


title: Blood_Platelets_Vumc-NSCLC-214-TR873


title: ROP_GRA_WT_31


title: Participant 10, timepoint 3

description: ex vivo whole blood

value: hr 6


title: Participant 10, timepoint 4

description: ex vivo whole blood

value: hr 9


title: Participant 10, timepoint 6

description: ex vivo whole blood

value: hr 15


title: ROP_GRA_WT_23

value: RH

value: tachyzoite


title: Blood_Platelets_Vumc-NSCLC-205-TR870


title: ROP_GRA_WT_22


title: Participant 10, timepoint 2

description: ex vivo whole blood

value: hr 3


title: ROP_GRA_WT_21


title: Blood_Platelets_NKI-NSCLC-107-660-TR751


title: ROP_GRA_WT_33


title: Participant 10, timepoint 1

description: ex vivo whole blood

value: whole blood


title: Blood_Platelets_NKI-NSCLC-107-395-TR749


title: ROP_GRA_WT_24


title: Blood_Platelets_NKI-NSCLC-107-162-TR748


title: ROP_GRA_WT_14


title: ROP_GRA_WT_13


title: Participant 09, timepoint 16

description: ex vivo whole blood

value: hr 45


title: ROP_GRA_P4_3


title: ROP_GRA_WT_15


title: ROP_GRA_WT_11


title: Blood_Platelets_NKI-NSCLC-107-602-TR747


title: ROP_GRA_P3_1


title: Blood_Platelets_NKI-NSCLC-107-419-TR745


title: Participant 09, timepoint 12

description: ex vivo whole blood

value: hr 33


title: Blood_Platelets_NKI-NSCLC-107-533-TR746


title: ROP_GRA_P4_1


title: NvEndo72hpf_10x_scRNA-seq

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: single cell RNA-seq data used to generate Endo-atlas

data_processing:
10x scRNA-seq: Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline (version4.0). Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using nematostella genome NV2. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Genome_build: NV2
Supplementary_files_format_and_content: Gene count table in csv file for RNA-seq data, single cell expression matrix in h5 format

organism: Nematostella vectensis

source_name: Endoderm isolate

growth_protocol: All animals used in this study were raised at 22°C

extract_protocol: 200 planula larvae were collected into a 1.5mL eppendorf tube. 500uL of TRIzol reagent was added to each tube and vortexed until samples is homogenized. Total mRNA extraction was performed using Directzol RNA Miniprep kits following manufacturer's instructions.

treatment_protocol: Anthox1a, Anthox8, Anthox6a mutants were generated using CRISPR/Cas9 (500ng/uL RNP complex). shRNAs targeting Pbx or carrying a scrambled sequence were injected at a final concentration of 600ng/uL into unfertilized oocytes.

value: Endoderm isolate

value: 72hpf planula

tag: genotype/variation

value: wildtype

tag: protocol

value: 10X scRNA-seq


title: Participant 09, timepoint 13

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 36


title: WT_shRNAcontrol_rep2_RNA-seq

description: Control for shRNA experiment

data_processing:
Bulk RNA-seq:Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.  Reads were then aligned to Nematostella genome NV2 using STAR. Raw reads count table was generated with FeatureCounts
Genome_build: NV2
Supplementary_files_format_and_content: Gene count table in csv file for RNA-seq data, single cell expression matrix in h5 format

source_name: Whole planula larvae

value: Whole planula larvae

value: Control shRNA injected larvae

value: PolyA Selected RNA-seq


title: ROP_GRA_library


title: Blood_Platelets_NKI-NSCLC-107-439-TR740

value: Thrombocytes

value: NSCLC


title: WT_shRNAcontrol_rep1_RNA-seq

description: Control for shRNA experiment


title: Participant 09, timepoint 11

description: ex vivo whole blood

value: hr 30


title: ROP_GRA_WT_16

value: RH

value: tachyzoite


title: Blood_Platelets_NKI-NSCLC-107-703-TR737


title: WT_72h_rep2_RNA-seq

description: Bulk RNA-seq data used to identify potential landmark genes


title: Participant 09, timepoint 15

description: ex vivo whole blood

value: whole blood

value: hr 42


title: ROP_GRA_WT_12


title: Participant 09, timepoint 14

description: ex vivo whole blood

value: hr 39


title: ROP_GRA_P4_2


title: Participant 09, timepoint 10

description: ex vivo whole blood

value: hr 27


title: WT_72h_rep1_RNA-seq

value: 72hpf planula


title: Blood_Platelets_NKI-NSCLC-107-183-TR735


title: WT_60h_rep2_RNA-seq

value: 60hpf planula

value: wildtype


title: Blood_Platelets_NKI-NSCLC-107-288-TR732


title: Participant 09, timepoint 8

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 21


title: WT_48h_rep1_RNA-seq

value: Whole planula larvae

value: 48hpf planula


title: Participant 09, timepoint 9

description: ex vivo whole blood

value: hr 24


title: Participant 09, timepoint 7

description: ex vivo whole blood

value: hr 18


title: WT_60h_rep1_RNA-seq

value: PolyA Selected RNA-seq


title: Pbx_sh1_rep1_RNA-seq

description: shRNA knockdown of Pbx

value: shPbx1 injected larvae


title: Pbx_sh2_rep2_RNA-seq

description: shRNA knockdown of Pbx

value: shPbx2 injected larvae


title: Participant 09, timepoint 6

description: ex vivo whole blood

value: hr 15


title: Blood_Platelets_NKI-NSCLC-107-577-TR731

value: Thrombocytes

value: NSCLC


title: Pbx_sh1_rep2_RNA-seq

description: shRNA knockdown of Pbx


title: Pbx_sh2_rep1_RNA-seq

description: shRNA knockdown of Pbx


title: Blood_Platelets_NKI-NSCLC-107-262-TR730


title: Blood_Platelets_NKI-NSCLC-107-642-TR726


title: Blood_Platelets_NKI-NSCLC-107-518-TR724


title: Anthox8_60h_rep2_RNA-seq

value: F3 Anthox8 homozygous mutant


title: Participant 09, timepoint 4

description: ex vivo whole blood

value: whole blood

value: hr 9


title: Anthox8_72h_rep2_RNA-seq

value: 72hpf planula


title: Blood_Platelets_NKI-NSCLC-107-162-TR723


title: Anthox8_60h_rep1_RNA-seq

value: 60hpf planula


title: WT_48_rep2_RNA-seq

value: wildtype


title: Anthox8_48h_rep2_RNA-seq


title: Participant 09, timepoint 3

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 6


title: Blood_Platelets_MGH-NSCLC-L122-TR715


title: Anthox8_48h_rep1_RNA-seq

value: Whole planula larvae

value: 48hpf planula


title: Participant 09, timepoint 2

description: ex vivo whole blood

value: hr 3


title: Anthox6a_72h_rep2_RNA-seq

value: F3 Anthox6a homozygous mutant

value: PolyA Selected RNA-seq


title: Anthox6a_72h_rep1_RNA-seq


title: Blood_Platelets_Vumc-NSCLC-189-TR713


title: Participant 09, timepoint 5

description: ex vivo whole blood

value: hr 12


title: Participant 09, timepoint 1

description: ex vivo whole blood

value: hr 0


title: Anthox6a_60h_rep2_RNA-seq


title: Anthox6a_60h_rep1_RNA-seq


title: Anthox8_72h_rep1_RNA-seq


title: Anthox6a_48h_rep1_RNA-seq


title: Participant 08, timepoint 16

description: ex vivo whole blood

value: hr 45


title: Anthox6a_48h_rep2_RNA-seq


title: Anthox1a_60h_rep2_RNA-seq

value: F3 Anthox1a homozygous mutant


title: Anthox1a_72h_rep2_RNA-seq


title: Blood_Platelets_Vumc-NSCLC-184-TR710

value: Thrombocytes

value: NSCLC


title: Anthox1a_72h_rep1_RNA-seq


title: Blood_Platelets_Vumc-NSCLC-131-TR709


title: Participant 08, timepoint 15

description: ex vivo whole blood

value: whole blood

value: hr 42


title: Anthox1a_60h_rep1_RNA-seq

value: 60hpf planula


title: Participant 08, timepoint 14

description: ex vivo whole blood

value: hr 39


title: Anthox1a_48h_rep1_RNA-seq


title: Anthox1a_48h_rep2_RNA-seq


title: Blood_Platelets_MGH-NSCLC-175-TR707


title: Participant 08, timepoint 13

description: ex vivo whole blood

value: Plasmodium vivax infected

value: hr 36


title: Participant 08, timepoint 12

description: ex vivo whole blood

value: hr 33


title: T3-3(basal diet + 2% succinate)

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

department: College of Animal Science and Technology

institute: Ningxia University

data_processing:
Illumina Casava1.7 software used for basecalling.
we use Cutadapt(v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）forfurther analysis .
Thefiltered reads were mapping to the reference genome using HISAT2 v2.1.0
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the originalexpression of the gene, and then used FPKM to standardize the expression.
Assembly: Genome:GCF_016772045.1_ARS-UI_Ramb_v2.0_genomic.fna    Path:https://www.ncbi.nlm.nih.gov/assembly/GCF_016772045.1  Genebuild by:NCBI
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Ovis aries

source_name: Tan sheep

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies)
Select total RNA >=1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina

tag: age

value: 5 month-old

tag: treatment

value: basal diet + 2% succinate


title: Blood_Platelets_Vumc-NSCLC-188-TR712


title: T3-2(basal diet + 2% succinate)


title: Blood_Platelets_Vumc-NSCLC-115-TR706


title: T3-1(basal diet + 2% succinate)


title: T2-3(basal diet + 1% succinate)

value: basal diet + 1% succinate


title: Blood_Platelets_Vumc-NSCLC-106-TR705


title: Participant 08, timepoint 11

description: ex vivo whole blood

tag: time

value: hr 30


title: Blood_Platelets_Vumc-NSCLC-185-TR711


title: T2-1(basal diet + 1% succinate)


title: T2-2(basal diet + 1% succinate)


title: Participant 08, timepoint 10

description: ex vivo whole blood

value: hr 27


title: Blood_Platelets_Vumc-NSCLC-164-TR691


title: Participant 08, timepoint 9

description: ex vivo whole blood

value: hr 24


title: T1-2(basal diet + 0.5% succinate)

value: basal diet + 0.5% succinate


title: Blood_Platelets_Vumc-NSCLC-160-TR690


title: C-3(basal diet)

value: basal diet


title: Participant 08, timepoint 7

description: ex vivo whole blood

value: hr 18


title: Participant 08, timepoint 8

description: ex vivo whole blood

value: hr 21


title: T1-1(basal diet + 0.5% succinate)


title: jcov97-cd14_S43_L001

city: New York

first: Jin-Gyu

last: Cheong

address: 1300 York Avenue

institute: Weill Cornell Medicine

description:
PCR amplicon
CD14_CP.csv

data_processing:
Paired-end Bulk ATAC-seq reads were quality trimmed using Trimmomatic.
trimmed reads were aligned to human genome (hg38) using BWA
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the consensus peak set was generated using the R package DiffBind. The consensus peakset was generated per celltype.
Peaks only present in at least two samples were included in the analysis. Raw read counts were normalized within the cinaR package.
Assembly: hg38
Supplementary files format and content: Normalized counts for Atacseq consensus peaks per tissue/cell type

source_name: PBMC

extract_protocol: As previously described in Corces, M.R. et al. 2017, PMID: 28846090

value: PBMC

value: CD14 Monocytes

tag: age (in_years)

tag: Sex

value: Female

tag: clinical status