title: WS4 SC-beta unedited

city: Saint Louis

first: Kristina

last: Maxwell

state: MO

address: 660 S. Euclid Ave. Campus Box 8127

department: Medicine

institute: WASHINGTON UNIVERSITY IN ST. LOUIS

data_processing:
All sequencing data were generated by the Washington University Genome Technology Access Center (GTAC)
Singe Cell RNA sequencing files were processed by Cell Ranger 2.1.1
Genome_build: h_sapien Ensembl_R76
Supplementary_files_format_and_content: Single cell RNA sequencing data presented as matrix files.

source_name: Stem cell-derived beta cells

growth_protocol: Cells were grown using the planar protocol as described in the submitted manuscript.

extract_protocol:
Single Cell RNA Seq: Cells processed during Stage 5 using Chromium Single Cell 3’ Library and Gel Bead  Kit v2 (10x Genomics, 120237)
Library construction for single cell was constructed using 10X Chromium Protocol.

treatment_protocol: Cells either contained a CRISPR/Cas9 correction (correction) or had presence of a pathogenic variant (unedited) causing Wolfram Syndrome.

value: iPS-Derived Beta Cells

tag: Stage

value: Stage 6

tag: phenotype

value: corrected by CRISPR/Cas9

tag: genotype allele 1

tag: genotype allele 2

value: c.1885C (corrected)


title: WS4 SC-beta corrected

status: Public on Apr 22 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: Wolfram Syndrome pathogenic variant


title: sgn3-3_100nM_CIF2_treatment_for_480min_batch1

city: Lausanne

first: Emanuel

last: Schmid-Siegert

address: UNIL Sorge

country: Switzerland

institute: UNIL

description: Samples were collected in March 2018 at Lausanne, Switzerland.

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v.0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Arabidopsis thaliana TAIR10 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using A. thaliana TAIR10 Ensembl 39 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include gene-level read counts for each sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana ecotype Col-0 was grown at 22 Celsius degree under 16 h light/8 h dark vertically on solid half-strength Murashige-Skoog medium with mesh for 5 days in the same percival after 2-day startification at 4 Celsius degree.

extract_protocol:
RNA was extracted using a Trizol-adapted Reliaprep RNA extraction kit (Promega).
RNA quality was assessed on a Fragment Analyzer (Advanced Analytical Technologies, Inc., Ankeny, IA, USA).  RNA-seq libraries were prepared using 1000 ng of total RNA  and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA)   using a PerkinElmer-developed automated script. Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents and  sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. Sequencing data were processed using the Illumina Pipeline Software version 2.20.

treatment_protocol: 5-day-old seedlings on mesh were transferred onto fresh half-strength medium with or without 100 nM CIF2 (Peptide Specialty Laboratories GmbH) for 30, 120, or 480 min. After the treatment, whole roots were collected and frozen in liquid nitrogen immediately.

tag: ecotype

tag: genotype

tag: treatment

value: 100 nM CIF2 for 480 min


title: 64_18WKS_C2

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

library_source: genomic

data_processing:
Library strategy: Bar-Seq
Barcode sequences were extracted with the TagDust software (v2.33)
Extracted barcode sequences were processed with an ad-hoc script to merge similar (erroneous) barcodes
Supplementary_files_format_and_content: Tab-separated matrix with barcode counts

molecule: genomic DNA

source_name: PBMCs from xenotransplanted NSG mice

extract_protocol:
QIAamp DNA Micro Kit (QIAGEN)
Custom library construction protocol. PCR amplicons for each individual sample were generated by nested PCR starting from >50-100 ng of purified gDNA. The first PCR step was performed with GoTaq Hot Start Polymerase (Promega) according to manufacturer instruction using the following amplification protocol: 95°C x 5’, (95°C x 0.5’, 60°C x 0.5’, 72°C x 0.5’) x 20 cycles, 72°C x 5’. Forward primers were designed to bind donor template upstream the BAR sequence, while the reverse primers annealed outside the homology region, thus amplifying 328 bp of the on-target integrated cassette. Exclusively for targeted sequencing of the transfer vector plasmid and AAV library, the reverse primer annealed to the downstream homology region. The second PCR step was performed with GoTaq G2 DNA Polymerase (Promega) according to manufacturer instruction using 5 µl of the first-step PCR product and the following amplification protocol: 95°C x 5’, (95°C x 0.5’, 60°C x 0.5’, 72°C x 0.5’) x 20 cycles, 72°C x 5’. Second-step PCR primers were endowed with tails containing P5/P7 sequence, i5/i7 Illumina tag to allow multiplexed sequencing and R1/R2 primer complementary sequence. PCR library amplicons were separately purified using MinElute PCR Purification kit (QIAGEN) and AmpPure XP beads (Invitrogen).
NextTera Illumina

value: Peripheral blood mononuclear cells

tag: timepoint

value: 18 wks post-transplant

tag: facs sorting

value: no


title: 64_18WKS_C1


title: 64_18WKS_C0


title: sgn3-3_100nM_CIF2_treatment_for_480min_batch3


title: 64_18WKS_B4


title: WT_100nM_CIF2_treatment_for_480min_batch2

value: Wildtype


title: 64_18WKS_B2


title: 64_18WKS_B1


title: WT_100nM_CIF2_treatment_for_480min_batch3


title: 16HBE14o- WT -20.9 [AH981]

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data were analyzed using 4cseq pipeline http://compgenomics.weizmann.ac.il/tanay/?page_id=367
Genome_build: hg19
Supplementary_files_format_and_content: The processed data is a dataframe each genomic fragment and its measured interaction frequency with the viewpoint of interest. The processed data can be used to plot a dominogram to visualized these interaction frequencies.

growth_protocol: Cells were grown in indicated media using standard methods

extract_protocol:
Nuclei were made as per the above Methods paper.
All libraries were constructed as per the above Methods paper.
4C-seq Barcoded libraries with Illumina sequencing adapters were made as per above Methods paper.

treatment_protocol: As per Splinter, E et al, 2012, Methods.

value: Human bronchial epithelial cells

value: Wild type

tag: growth media

value: DMEM + 10% FBS


title: 64_18WKS_B0


title: WT_100nM_CIF2_treatment_for_30min_batch1

value: 100 nM CIF2 for 30 min


title: 64_18WKS_A4


title: del-44 cl.4 -80.1 [AH959]

value: CRISPR/Cas9 mediated deletion of -44 kb CRE from the CFTR locus in 16HBE14o- clone # 4


title: 64_18WKS_C3


title: 64_18WKS_A3


title: WT_100nM_CIF2_treatment_for_480min_batch1


title: 64_18WKS_A2


title: 64_18WKS_A0


title: del-35 cl.6 -80.1 [AH956]

value: CRISPR/Cas9 mediated deletion of -35 kb CRE from the CFTR locus in 16HBE14o- clone # 6


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_120min_batch3

value: cif1-2_cif2-2 (both are CRISPR alleles)

value: 100 nM CIF2 for 120 min


title: 64_12WKS_D4

value: 12 wks post-transplant


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_120min_batch2


title: 64_12WKS_D3


title: del-35 cl.6 Promoter [AH955]

source_name: del-35 cl.6 Promoter


title: del-44 cl.4 Promoter [AH958]

source_name: del-44 cl.4 Promoter


title: 64_18WKS_A1


title: 16HBE14o- WT -80.1 [AH917]


title: 16HBE14o- WT +48.9 [AH982]


title: 64_18WKS_B3


title: 64_12WKS_D2


title: sgn3-3_100nM_CIF2_treatment_for_120min_batch3


title: 64_12WKS_D0


title: cif1-2_cif2-2_100nM_CIF2_treatment_for_120min_batch1


title: 64_12WKS_D1


title: 64_12WKS_C3


title: 16HBE14o- WT promoter [AH916]

source_name: 16HBE14o- WT promoter


title: 64_12WKS_C2


title: sgn3-3_100nM_CIF2_treatment_for_120min_batch2


title: del-44 cl.4 +48.9 [AH1044]


title: 64_12WKS_C0


title: 64_12WKS_C1


title: 64_12WKS_B3


title: del-44 cl.4 -20.9 [AH1043]


title: 64_12WKS_B4


title: 64_12WKS_B2


title: WT_100nM_CIF2_treatment_for_120min_batch3


title: del-35 cl.6 +48.9 [AH1009]


title: 64_12WKS_B1


title: del-35 cl.6 -20.9 [AH1008]


title: WT_100nM_CIF2_treatment_for_120min_batch2


title: 64_12WKS_B0


title: Calu3 WT -80.1 [AH1004]

source_name: Calu3 WT -80.1

value: Human Lung adenocarcinoma cell line


title: WT_100nM_CIF2_treatment_for_120min_batch1


title: 64_12WKS_A3


title: 64_12WKS_A2


title: Calu3 WT promoter [AH1003]

source_name: Calu3 WT promoter


title: 16HBE14o- RNAPII ChIP-seq

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data was analyzed using ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: human bronchial epithelial cell line

growth_protocol: Cells were grown in indicated medias using standard methods.

extract_protocol:
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protease Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with antibodies.
DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5’ adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPure XP beads. Sequencing was performed on an Illumina Hi-Seq.

tag: cell line

tag: chip antibody

value: RNA polymerase II (RNAPII) Rpb1 NTD (D8L4Y) (Cell Signaling 14958S)


title: 64_8WKS_D3

value: 8 wks post-transplant


title: 64_12WKS_A0


title: 64_12WKS_A1


title: Caco-2, pks_minus_E.coli_rep4

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

data_processing:
Library strategy: BLISS-seq
Raw sequencing data were pre-processed as previously described (Yan W, et al. Nat Commun, 2017). In brief, only reads which contained the expected prefix of UMI and sample barcode were kept using SAMtools. One mismatch in the barcode sequence was allowed. Reads from each library were split by barcode and prefixes were trimmed.
After demultiplexing and trimming,  the remaining sequences were aligned to the GRCh37/hg19 reference genome using BWA-MEM. Reads with mapping quality scores ≤ 30 and those which were determined as PCR duplicates were removed.
Finally, a BED file containing a list of unique DSBs locations was generated. DSBs which fell into ENCODE blacklist regions, high coverage regions and low mappability regions were removed. Kept positions of DSBs were further used in downstream analysis. Start and end corrdinates in BED files denote the two nucleotides on both sides of the DSB position.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain unique genomic locations of observed double-strand breaks.  Columns 1-3 contain chromosome, start and end of the breakpoint in GRCh37 coordinates.  Breakpoints are located between start and end position. The fourth field contains the number of reads and, after the colon, a list of all unique UMIs observed for a given breakpoint. Column 5: dummy score; Column 6: genomic strand to which reads were mapped.

source_name: Caco-2, pks_minus_E.coli

growth_protocol: Caco-2 cells (from ATCC® HTB-37™) were cultured at 37 °C under a water-saturated 5% CO2 atmosphere, in DMEM medium (Life Technologies, cat. number: 10938-025), supplemented with 20% FCS (Biochrom, cat. number: S0115).

extract_protocol:
Cells were treated/infected in culture dishes and afterwards trypsinized, counted, centrifuged and resuspended in pre-warmed medium to obtain 10e6 cells per 1 ml. Then, cells were fixed by adding 16% PFA (Electron Microscopy Sciences, cat. number: 15710) to reach a final concentration of 4%. After 10 minutes, 2 M glycine (Molecular Dimensions, cat. number: MD2-100-105) was added to a final concentration of 125 mM in order to block unreacted aldehydes. This was followed by two 5 minutes incubations, first at room temperature and then on ice, followed by two washes in ice-cold PBS. Cross-linked cells were stored in PBS at 4 °C until further processing.
Fixed cells were lysed with mild buffers. Further DSBs were blunted and BLISS adapters ligated. Next, genomic DNA was extracted, sonicated and DSB ends were amplified with in vitro transcirption, after which generated RNA was used to Illumina small RNA-like library preparation protocol (similar as desribed for sBLISS: Gothe H., et al. Mol Cell, 2019).

treatment_protocol: To infect Caco-2 cells, overnight liquid culture of E.coli strain M1/5 (Streptomycin-resistant and colibactin-positive) and E.coli strain M1/5::ΔclbR (streptomycin-resistant and colibactin-negative) was set up. Bacteria were inoculated in 5 ml of Luria broth (LB) medium and incubated overnight at 37 °C in a shaking incubator. The overnight inoculum was diluted 1:33 in infection medium (DMEM + 10% FCS + HEPES (Life Technologies, cat. number: 15630-056)) to obtain OD600=1 after 3 h of incubation to give 1.5 × 10e9 bacteria/ml. Prepared bacteria inoculum was further diluted to reach MOI 20, added to Caco-2 cells seeded previously and incubated for 3 hours at 37 °C. Medium was then aspirated and cells fixed according to the BLISS protocol. For every biological replicate positive (etoposide-treatment) and negative (no treatment) controls were included. Etoposide powder (Sigma Aldrich, cat. number: E1383) was diluted in DMSO in order to reach 50 mM working solution. Aliquots of the drug were stored at −20 °C. Final drug dilutions to the concentration of 50 μM were performed in pre-warmed infection medium prior to each drug exposure. Treatment was conducted for 3 hours at 37 °C and afterwards medium was aspirated and etoposide-treated cells were fixed in the same way as E. coli-infected cells.

value: pks- E.coli infection (MOI20, 3hr)

tag: biological replicate

tag: barcode

value: AGCCATCA

tag: library


title: 64_8WKS_D4

value: Peripheral blood mononuclear cells


title: Caco-2, etoposide_rep4

source_name: Caco-2, etoposide

value: etoposide (50uM, 3hr)

value: CTAACGAG


title: 64_8WKS_D2

value: no


title: Caco-2, pks_plus_E.coli_rep4

source_name: Caco-2, pks_plus_E.coli

value: pks+ E.coli infection (MOI20, 3hr)

value: GCTTGTCA


title: sgn3-3_100nM_CIF2_treatment_for_120min_batch1


title: 16HBE14o- H3K27Ac ChIP-seq

value: Human bronchial epithelial cells

value: DMEM + 10% FBS

value: H2K27ac (Millipore 07-360)


title: 64_8WKS_D0


title: Caco-2, no_treatment_rep4

source_name: Caco-2, no_treatment

value: no-treatment

value: GCTTGGAG


title: 16HBE14o- Omni ATAC rep2

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data was analyzed using ENCODE pipeline https://github.com/kundajelab/atac-seq-pipeline
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: 16HBE14o- Omni ATAC

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were constructed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exception: Final libraries were purified with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transposition.


title: 64_8WKS_C3


title: Caco-2, pks_minus_E.coli_tech_rep2

value: Technical replicate of biological replicate 2

value: TGATGATC


title: 64_8WKS_C2


title: 16HBE14o- Omni ATAC rep1


title: 64_12WKS_A4

value: 12 wks post-transplant


title: Caco-2, pks_plus_E.coli_tech_rep2

value: ACGACATC


title: 64_8WKS_B4

value: 8 wks post-transplant


title: 64_8WKS_C0


title: Donor 3 CD26- CD94lo (D3 DN)

city: Melbourne

first: Hyon Xhi

last: Tan

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

country: Australia

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

description: Sample 12

data_processing:
RNAseq analysis was performed using the web-based Galaxy platform maintained by Melbourne Bioinformatics.
Reads were mapped to the Homo sapiens reference genome (hg19) using HISAT2 and reads were quantified using HTSeq.
Count matrices were generated and inputted into Degust (http://degust.erc.monash.edu) for final data analysis and visualization. The Degust Voom/Limma method was selected for data processing.
Genome_build: hg19
Supplementary_files_format_and_content: Degust_Voom_Limma.csv: Normalized abundance measurements - Degust output
Supplementary_files_format_and_content: Raw_counts_all_subsets.txt: Raw counts -- HTseq

source_name: Human PBMC

extract_protocol:
RNA was isolated from sorted cells using a QIAGEN RNeasy Plus Micro Kit, as per manufacturer's protocol.
Illumina Truseq Stranded mRNA kit was use for library construction. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: PBMC

value: CD3+ Vd2+ CD26- CD94lo


title: Donor 3 CD26+ CD94lo (D3 26)

description: Sample 11

value: CD3+ Vd2+ CD26+ CD94lo


title: 64_8WKS_B3

value: Peripheral blood mononuclear cells


title: 64_8WKS_B2

value: no


title: Caco-2, no_treatment_tech_rep2

value: CATCAATC


title: 64_8WKS_A4


title: Donor 3 CD26- CD94hi (D3 94)

description: Sample 10

value: CD3+ Vd2+ CD26- CD94hi


title: 64_8WKS_A3


title: 64_8WKS_D1


title: Caco-2, pks_minus_E.coli_rep3

value: pks- E.coli infection (MOI20, 3hr)


title: 64_8WKS_B0


title: 64_8WKS_A2


title: 64_8WKS_B1


title: Caco-2, pks_plus_E.coli_rep3

value: pks+ E.coli infection (MOI20, 3hr)


title: 64_8WKS_A1


title: Donor 2 CD26- CD94lo (D2 DN)

description: Sample 8


title: Donor 2 CD26+ CD94lo (D2 26)

description: Sample 7


title: Caco-2, etoposide_rep3

value: etoposide (50uM, 3hr)

value: GTCGTATC


title: 64_8WKS_C1


title: 64_8WKS_A0


title: Donor 2 CD26- CD94hi (D2 94)

description: Sample 6


title: 6 hour concanamycin A treatment [14517X12]

city: Salt Lake City

first: Adam

middle: L

last: Hughes

state: Utah

address: 15 N Medical Drive East, RM 4100

department: Biochemistry

institute: University of Utah School of Medicine

data_processing:
Sequence reads were trimmed and aligned using STAR (v2.5.2b), with --alignIntronMax set to 2000, –twopassMode set to Basic, and --clip3pAdapterSeq set to AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Aligned reads were counted using featurecounts (v1.5.1), setting -s equal to 2 for a reversely stranded library.
Genome_build: S. cerevisiae R64-1-1 Ensembl release 90
Supplementary_files_format_and_content: excel file of raw counts

organism: Saccharomyces cerevisiae

source_name: wild type yeast

growth_protocol: Yeast were grown exponentially for 16 hours prior to drug treatment and were kept in the exponential phase (less than 8 million cells/ml) for the duration of the experiment. The experiment was carried out in YPD media.

extract_protocol:
Cells were lysed by micro-bead beating and RNA was purified with Qiagen's Rneasy mini purification kit. Contaminating DNA was removed by on column Rnase-free Dnase (Qiagen) treatment.
Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold rRNA Removal Kit Yeast (Illumina MRZY1306) to substantially deplete rRNA from the samples. Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Kit. Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay. The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit. Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.

treatment_protocol: Yeast were treated with 500 nM concanamycin A for 0, 1, 3, or 6 hours

tag: strain

tag: hours treated


title: Caco-2, etoposide_tech_rep2


title: Donor 2 CD26+ CD94hi (D2 DP)

description: Sample 5

value: CD3+ Vd2+ CD26+ CD94hi


title: 6 hour concanamycin A treatment [14517X11]


title: Caco-2, pks_minus_E.coli_rep2


title: TOD_synthetic

city: Stanford

first: Rhiju

last: Das

state: California

address: 279 Campus Dr, B419 Beckman Center

institute: Stanford University School of Medicin

data_processing:
Raw sequencing files were demultiplexed using novobarcode.
For M2-seq analysis of the HIV 3' UTR construct, the demultiplexed files were run through the ShapeMapper software, and the resulting mutational profile strings were run through the M2-seq analysis pipeline (further details can be found at: https://github.com/ribokit/m2seq) to yield the final two-dimensional reactivity files.
For polyA length analysis, raw demultiplexed reads were analyzed with custom python scripts that directly searched for polyAs surrounded by constant flanking regions. For more information see: https://github.com/DasLab/Anomalous_polyA_RT.
For reactivity analysis, the demultiplexed reads were analyzed with the RNAFramework, ShapeMapper, and ShapeMapper2 pipelines. Custon python scripts were then used to compare computed reactivities between packages.
For more information see: https://github.com/DasLab/Anomalous_polyA_RT.
genome build: GGGTACAAAAAAAAAAAGTACAAAGAAACAACAACAACAAC
Supplementary_files_format_and_content:
For HIV 3'UTR M2-seq analysis: mutation strings indicating the location of mutations for each read are provided in the format of one read per line in a one-hot encoding. Two-dimensional reactivity files are provided in the RDAT file format as specified here: https://rmdb.stanford.edu/deposit/specs/.
For polyA length analysis, CSV tables are provided for each construct, with each column representing data relevant to a single condition (e.g. reverse transcribed with TGIRT). Values in each cell represent the raw number of reads corresponding to a given polyA length. For insertion/substitution tables, the frequency of an insertion or substitution at each nucleotide along the polyA tail (read in 3' to 5' direction).
For reactivity analysis, each plain text file contains the reactivity of a construct for a given condition. Each line contains a reactivity score of a single nucleotide position.

organism: synthetic construct

source_name: chemically synthesized

growth_protocol: RNA was chemically synthesized using 2′-tBDSilyl protected phosphoramidite monomers.

extract_protocol: Chemically synthesized RNA was desalted with a Gel-Pak 1.0 desalting column (Glen Research) and concentrated with a SpeedVac (Thermo Fisher Scientific) on low heat. Concentrated RNA was checked for appropriate molecular weight with the Voyager-DE STR Biospectrometry Workstation (Applied Biosystems) and a MALDI-TOF mass spectrometer (Applied Biosystems). Quality-verified RNA was finally size selected using a denaturing 10% PAGE gel.

treatment_protocol: Methylations were introduced during the chemical synthesis with the addition of methylated monomers at the appropriate synthesis cycle.

tag: sample type

value: in vitro transcribed

tag: library type

value: pooled

tag: adapter strategy

value: direct ligation

tag: rna modification

value: Methylation


title: TOD_MapSeq

data_processing:
Raw sequencing files were demultiplexed using novobarcode.
For M2-seq analysis of the HIV 3' UTR construct, the demultiplexed files were run through the ShapeMapper software, and the resulting mutational profile strings were run through the M2-seq analysis pipeline (further details can be found at: https://github.com/ribokit/m2seq) to yield the final two-dimensional reactivity files.
For polyA length analysis, raw demultiplexed reads were analyzed with custom python scripts that directly searched for polyAs surrounded by constant flanking regions. For more information see: https://github.com/DasLab/Anomalous_polyA_RT.
For reactivity analysis, the demultiplexed reads were analyzed with the RNAFramework, ShapeMapper, and ShapeMapper2 pipelines. Custon python scripts were then used to compare computed reactivities between packages.
For more information see: https://github.com/DasLab/Anomalous_polyA_RT.
genome build:
S1:GGAAAAGGCGTCGAGTAGACGCCAACAACGGAAACCTGAAAGATCAAAAAAAAAAAGATCAAGTACAAAAAAAAAAAGTACAACAGGAAAAAAAAAAAGCATAGGTTCGCCTATGCAAACCAAACCGTCAGCGAGTAGCTGACAAAAAGAAACAACAAC,
S7:GGAAAAGGCGTCGAGTAGACGCCAACAACGGAAACCTGAAAGATCAAAAAACAAAAGATCAAGTACAAAAAACAAAAGTACAACAGGAAAAAACAAAAGCATAGGTTCGCCTATGCAAACCAAACCGTCAGCGAGTAGCTGACAAAAAGAAACAACAACAACAAC
Supplementary_files_format_and_content:
For HIV 3'UTR M2-seq analysis: mutation strings indicating the location of mutations for each read are provided in the format of one read per line in a one-hot encoding. Two-dimensional reactivity files are provided in the RDAT file format as specified here: https://rmdb.stanford.edu/deposit/specs/.
For polyA length analysis, CSV tables are provided for each construct, with each column representing data relevant to a single condition (e.g. reverse transcribed with TGIRT). Values in each cell represent the raw number of reads corresponding to a given polyA length. For insertion/substitution tables, the frequency of an insertion or substitution at each nucleotide along the polyA tail (read in 3' to 5' direction).
For reactivity analysis, each plain text file contains the reactivity of a construct for a given condition. Each line contains a reactivity score of a single nucleotide position.

source_name: in vitro transcribed

growth_protocol: RNA was transcribed using DNA templates containing a T7 RNA Polymerase promoter sequence at their 5´ ends and a 20 base-pair Tail2 sequence at their 3´ ends (Supplemental File, sequences.xlsx). The RNA sequence consisted of the sequence of interest flanked by a reference hairpin on each side serving as internal structural controls.  The DNA template was assembled through DNA primer assembly using primers designed using the Primerize tool (https://primerize.stanford.edu/). Designed primers were ordered in plate format from Integrated DNA Technologies (IDT) and assembled via PCR assembly with Phusion DNA polymerase as described on the Primerize PCR Assembly Protocol (https://primerize.stanford.edu/protocol/#PCR). Assembly products were verified for size via agarose gel electrophoresis and subsequently purified using Agencourt RNAClean XP beads. Purified DNA was quantified via NanoDrop (Thermo Scientific) and 8 pmol of purified DNA was then used for in vitro transcription with T7 RNA polymerase (New England Biolabs Inc.).

extract_protocol:
Enzymatically synthesized RNA was purified with Agencourt RNAClean XP beads.
Reverse transcription and ligation of the second Illumina sequencing adapter was carried out as previously described (Cheng et al. 2015, eLife). Briefly, reverse transcription was carried out with primers containing an RTB barcode and Illumina . The RTB barcode assigned to each sample and the sequence of each RTB barcoded reverse transcription primer are listed in Supplemental File sequences.xlsx. For the second adapter ligation, P_TruSeqAdapt01_p and P_TruSeqAdapt02_p ligation primers were used for TOD-S1 and TOD-S7 constructs, respectively (see Supplemental File sequences.xlsx). Sequencing libraries were quantified by qPCR and sequenced on an Illumina MiSeq using a 150-cycle v3 chemistry kit per manufacturer’s instructions, with 35 and 121 cycles used for read 1 and read 2, respectively.

treatment_protocol: 1.2 pmol of RNA was denatured in 50 mM Na-HEPES pH 8.0 at 90 ℃ for 3 minutes and cooled at room temperature for 10 minutes. The RNA was then folded with the addition of MgCl2 to a final concentration of 10 mM in 15 μL and incubated at 50 ℃ for 30 minutes, then left at room temperature for 10 minutes. For chemical modification of folded RNA, fresh working stocks of dimethyl sulfate (DMS, Sigma-Aldrich) and 1-methyl-7-nitroisatoic anhydride (1M7) were prepared. For DMS, 1 μL of DMS was mixed with 99 μL of 100% EtOH. The 100 μL solution was then added to 100 μL RNase free H2O for a final volume of 200 μL. For 1M7, 4.24 mg of 1M7 was dissolved in 1 mL of anhydrous DMSO. In the modification step, 5 μL of modifying agent (either DMS or 1M7) working stock was added to 15 μL of folded RNA and incubated at room temperature for 15 minutes. Modification reactions were quenched with 5 μL of quenching solution (β-mercaptoethanol or 0.5 M Na-MES pH 6.0 for DMS and 1M7, respectively).

value: Methylation or 2'-hydroxyl acylation


title: 6 hour concanamycin A treatment [14517X10]


title: 3 hour concanamycin A treatment [14517X9]


title: Caco-2, pks_plus_E.coli_rep2

value: ACGACATC


title: Donor 1 CD26- CD94lo (D1 DN)

description: Sample 4

value: PBMC

tag: cell type

value: CD3+ Vd2+ CD26- CD94lo


title: Donor 3 CD26+ CD94hi (D3 DP)

description: Sample 9


title: Caco-2, etoposide_rep2

tag: treatment


title: Donor 1 CD26+ CD94lo (D1 26)

description: Sample 3

value: CD3+ Vd2+ CD26+ CD94lo


title: 3 hour concanamycin A treatment [14517X7]


title: 1 hour concanamycin A treatment [14517X6]


title: 3 hour concanamycin A treatment [14517X8]


title: Caco-2, pks_minus_E.coli_rep1

value: TGATGATC


title: Caco-2, no_treatment_rep2

value: no-treatment

value: CATCAATC


title: 1 hour concanamycin A treatment [14517X4]


title: Caco-2, no_treatment_rep3


title: Donor 1 CD26+ CD94hi (D1 DP)

description: Sample 1


title: 0 hour concanamycin A treatment [14517X2]


title: 0 hour concanamycin A treatment [14517X3]


title: 0 hour concanamycin A treatment [14517X1]


title: Caco-2, etoposide_rep1


title: Caco-2, no_treatment_rep1


title: Animal 8, tumor 1, time 12

city: Sao Paulo

first: Flavio

last: Lichtenstein

state: São Paulo

address: Vital Brazil Ave., 1500

department: CDI - Inovation

country: Brazil

institute: Instituto Butantan

description:
A8T1h12
Equus caballus (ECA)
mRNA
case-12h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie2 and Hisat2 aligner were used for the first map and quality assess.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic.
Reads were mapped and quantified using Subread (featurecounts).
Transcripts were normalized and DEGs calculated using edgeR. DEGs are defined as genes LFC >= 1, FDR < .05.
Genome_build: Equus caballus (version 89)
Supplementary_files_format_and_content: subread_processed_less_2cols_Horse_Melanoma.tsv: Tab-delimited text files include CPM values for each sample.

organism: Equus caballus

source_name: horse melanoma tumor

extract_protocol:
Excision of in vivo melanoma tumors for histology and transcriptomics.
Total RNA was isolated from cultured cells with Trizol (Ambion, Life Technologies) and purified with an RNAspin Mini kit (GE Healthcare) according to the manufacturer's instructions, with extended treatment with DNase I for 1 h. RNA quality was evaluated with an Agilent 2100 Bioanalyzer RNA Pico assay. RNA was quantified by Quant-iT RiboGreen RNA reagent and Kit (Invitrogen, Life Technologies). Messenger RNA (mRNA) was isolated and used to prepare the complementary DNA (cDNA) libraries following TruSeq RNA Sample Prep Kit V2 (Illumina, San Diego, CA) instructions. Briefly, mRNA was isolated with oligo-dT and purified. Then mRNA was fragmented by heating at 94°C (4 min) in fragmentation buffer. Double-stranded cDNA was synthesized, end-repaired and A-tailed. Sequencing adapters were then ligated to cDNA fragments, according to the manufacturer’s protocol. cDNAs fragments were enriched after 15 cycles of PCR amplification. Library quality control was evaluated by the size distribution of the cDNA libraries measured by 2100 Bioanalyzer with DNA1000 assay (Agilent Technologies) and an ABI StepOnePlus Real-Time PCR System was used for quantification of the sample library before sequencing.
All 18 cDNA libraries were sequenced on Illumina HiSeq 1500 System, into a rapid paired-end flowcell in 200 cycles of 2x101 bp paired-end strategy.

treatment_protocol: We injected Amblyomin-X intratumorally, at 1 mg/kg of the tumor mass, and extracted the tumors after 6h and 12h – as control we injected PBS at 0h.

value: Melanoma tumor

value: Amblyomin-X

tag: time point

tag: animal


title: Animal 9, tumor 2, time 12

description:
A9T2h12
Equus caballus (ECA)
mRNA
case-12h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Animal 7, tumor 1, time 12

description:
A7T1h12
Equus caballus (ECA)
mRNA
case-12h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Animal 6, tumor 3, time 6

description:
A6T3h6
Equus caballus (ECA)
mRNA
case-6h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Animal 6, tumor 2, time 6

description:
A6T2h6
Equus caballus (ECA)
mRNA
case-6h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Animal 5, tumor 3, time 6

description:
A5T3h6
Equus caballus (ECA)
mRNA
case-6h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Donor 1 CD26- CD94hi (D1 94)

description: Sample 2

value: CD3+ Vd2+ CD26- CD94hi


title: OmniATAC-seq_MM165_BL

city: Leuven

first: Stein

last: Aerts

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
Data processing of human melanoma baseline OmniATAC-seq samples: Paired-end reads were mapped to the human genome (hg19-Gencode v18) using bowtie2 (v2.2.6). Mapped reads were sorted using SAMtools (v1.8) and duplicates were removed using Picard MarkDuplicates (v1.134). Reads were filtered by removing chromosomal reads and filtering for Q>30 using SAMtools. Bam files of technical replicates of the same cell line were merged at this point using samtools merge. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and --extsize 150 per sample. Chromosomal peaks, blacklisted regions (ENCODE) and peaks overlapping with alternative chromosomes were removed. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing human chromosome sizes. Peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score by keeping the peak with the highest score. For visualisation in IGV, normalised bigWigs were made by bamCoverage (Deeptools, v3.3.1), using as parameters --normalizeUsing None, -bl EncodeBlackListedRegions --effectiveGenomeSize 2913022398 and as scaling parameter (-scaleFactor) 1/(RIP/1E6), where the RIP stands for the number of reads in peaks.
Data processing of non-human (Omni)ATAC-seq samples, and of human SOX10 and TFAP2A knock-down OmniATAC-seq data: Adapter sequences were trimmed from the fastq files using fastq-mcf (as part of eautils; v1.05) and the read quality was checked using FastQC (v0.11.8). Reads were mapped using STAR (v2.5.1b) (for the zebrafish samples paired-end reads were mapped) to the genome which were downloaded from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/) (for human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10) and by applying the parameters --alignIntronMax 1 and --aslignIntronMin 2. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and with the genome size for the correct species in --g, and this for each sample per species separately. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing the chromosome sizes for the specific species. Per sample, peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score (keeping the highest scoring peak). Normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.28.0) using as scaling parameter (-scale) 1E6/(number of non-chromosomal mapping reads). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs, which were used in IGV for visualisation.
Genome_build: For human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10.
Supplementary_files_format_and_content: bigWig files represent the coverage of the ATAC-seq signal.

source_name: Melanoma cell line

growth_protocol:
Cells were cultured at 37°C with 5% CO2 and were maintained in Ham's F10 nutrient mix (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 µg ml-1 penicillin/streptomycin (Thermo Fisher Scientific).
Mentioned per sample in the SAMPLE section.

extract_protocol:
Cells were washed, trypsinised, spun down at 1000 RPM for 5 min, medium was removed and the cells were resuspended in 1 mL medium. Cells were counted and experiments were only continued when a viability of above 90% was observed. 50,000 cells were used per sample. OmniATAC-seq was performed as described previously in Corces et al., 2017; and ATAC-seq as described in Buenrostro et al., 2015.
Library prep was performed as described before in Corces et al., 2017 for OmniATAC-seq samplas; and as in Buenrostro et al., 2013 for ATAC-seq samples.

treatment_protocol: For the knock-down data: SOX10, TFAP2A and the control knockdown was performed in MM001 using respectively a SMARTpool of four siRNAs against, respectively, SOX10 (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00-0005, Dharmacon), TFAP2A (SMARTpool: ON-TARGETplus TFAP2A siRNA, number L-006348-02-0005, Dharmacon) and a negative control pool (ON-TARGETplus non-targeting pool, number D-001810-10-05, Dharmacon) at a concentration of 20 nM for SOX10-KD, and 40 nM for TFAP2A-KD and the control using as medium Opti-MEM (Thermo Fisher Scientific) and omitting antibiotics. The cells were incubated for 72 h before processing.

tag: tissue type

value: Cutaneous melanoma

tag: condition

value: Baseline


title: 1 hour concanamycin A treatment [14517X5]


title: Caco-2, pks_plus_E.coli_rep1

tag: cell line

value: pks+ E.coli infection (MOI20, 3hr)


title: Animal 4, tumor 2, time 6

description:
A4T2h6
Equus caballus (ECA)
mRNA
case-6h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Animal 4, tumor 1, time 6

description:
A4T1h6
Equus caballus (ECA)
mRNA
case-6h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: OmniATAC-seq_MM164_BL


title: OmniATAC-seq_MM122_BL


title: OmniATAC-seq_MM163_BL


title: Animal 5, tumor 1, time 6

description:
A5T1h6
Equus caballus (ECA)
mRNA
case-6h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Animal 3, tumor 4, time 0

description:
A3T4h0
Equus caballus (ECA)
mRNA
control
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv

value: Control (PBS)


title: Animal 3, tumor 3, time 0

description:
A3T3h0
Equus caballus (ECA)
mRNA
control
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: OmniATAC-seq_MM118_BL


title: Animal 7, tumor 3, time 12

description:
A7T3h12
Equus caballus (ECA)
mRNA
case-12h
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Animal 2, tumor 1, time 0

description:
A2T1h0
Equus caballus (ECA)
mRNA
control
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: Animal 1, tumor 2, time 0

description:
A1T2h0
Equus caballus (ECA)
mRNA
control
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: OmniATAC-seq_MM116_BL


title: HIV_3UTR

data_processing:
Raw sequencing files were demultiplexed using novobarcode.
For M2-seq analysis of the HIV 3' UTR construct, the demultiplexed files were run through the ShapeMapper software, and the resulting mutational profile strings were run through the M2-seq analysis pipeline (further details can be found at: https://github.com/ribokit/m2seq) to yield the final two-dimensional reactivity files.
For polyA length analysis, raw demultiplexed reads were analyzed with custom python scripts that directly searched for polyAs surrounded by constant flanking regions. For more information see: https://github.com/DasLab/Anomalous_polyA_RT.
For reactivity analysis, the demultiplexed reads were analyzed with the RNAFramework, ShapeMapper, and ShapeMapper2 pipelines. Custon python scripts were then used to compare computed reactivities between packages.
For more information see: https://github.com/DasLab/Anomalous_polyA_RT.
genome build:
GGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGT
ACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAAAAAAAAAAAAAAAAAAAAAAAGAAACAACAACAACAAC
Supplementary_files_format_and_content:
For HIV 3'UTR M2-seq analysis: mutation strings indicating the location of mutations for each read are provided in the format of one read per line in a one-hot encoding.
Two-dimensional reactivity files are provided in the RDAT file format as specified here: https://rmdb.stanford.edu/deposit/specs/.
For polyA length analysis, CSV tables are provided for each construct, with each column representing data relevant to a single condition (e.g. reverse transcribed with TGIRT). Values in each cell represent the raw number of reads corresponding to a given polyA length. For insertion/substitution tables, the frequency of an insertion or substitution at each nucleotide along the polyA tail (read in 3' to 5' direction).
For reactivity analysis, each plain text file contains the reactivity of a construct for a given condition. Each line contains a reactivity score of a single nucleotide position.

organism: Human immunodeficiency virus

extract_protocol:
Enzymatically synthesized RNA was purified with Agencourt RNAClean XP beads.
4.6 μL of the RNA sample was used to generated cDNA with SuperScript II reverse transcriptase with Mn2+ as the divalent ion to promote incorporation of mismatches or deletions across bypassed methylations. Reverse transcription reactions included 0.02 μM primer in final volume 12 μL; buffer of 25 mM Tris-HCl, pH 8.3, 75 mM KCl, 6 mM MnCl2, 5 mM DTT; and incubation of at 42 °C for 3 hrs. Reverse transcription reactions were stopped with 5 μL of 0.4 M sodium hydroxide at 90 °C for 3 min. Reactions were neutralized with acid quench (2 volumes 5 M NaCl, 2 volumes 2 M HCl, and 3 volumes of 3 M Na–acetate). cDNA was purified with Agencourt Ampure beads supplemented with PEG-8000, and purified cDNA was resuspended in 12.5 μL of RNase free water. 2.5 μL of cDNA was used for PCR with Illumina adapters (see Supplemental File sequences.xlsx). We found it necessary to perform emulsion PCR. For these reactions, we prepared an oil phase system composed of ABIL EM90, (Evonika) 80 μL, Triton X-100, 1.0 μL, and mineral oil, 1919 μL. Reactions combined 300 μL of this oil phase with 50 μL PCR mixture, composed of Phusion DNA polymerase, 1x Phusion buffer, 10 mM dNTPs, and 2 μM of each forward and reverse primer. We performed PCR at 98 °C, 30 sec-1 cycle; then 22 cycles of 98 °C for 10 sec, 64 °C for 30 sec, 72 °C for 30 sec; and 72 °C for 10 min for 1 cycle. The resulting dsDNA was purified by gel extraction and purification in Qiagen Qiaquick purification spin columns. The dsDNA was quantified with a Qubit instrument with the HS dsDNA kit.

treatment_protocol: 12.5 pmol of RNA was heated at 95 °C for 2 min; cooled on ice for 1 min; then incubated in 300 mM Na-cacodylate, pH 7.0, 10 mM MgCl2 at 37 °C for 30 min at a final volume of 25 μL. Modification conditions used were 0.17 M of dimethyl sulfate at 37 °C for 6 min. RNAse free water was added instead as a no modification control. DMS reactions were quenched with 25 μL of β-mercaptoethanol.

value: in vitro transcribed

value: pooled

value: PCR


title: OmniATAC-seq_MM052_BL


title: Animal 1, tumor 1, time 0

description:
A1T1h0
Equus caballus (ECA)
mRNA
control
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: SNU-520-3

type: RNA

city: Seoul

first: Yong-Min

last: Huh

address: 50 Shinchon-ro

country: South Korea

institute: Yonsei University

hyb_protocol: HumanHT-12 v3.0 Expression BeadChip array (Illumina) was used.

scan_protocol: Standard Illumina scanning protocol

data_processing: R limma package, neqc function (quantile normalization)

label: biotin

source_name: SNU-520 Cell Line

label_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for synthesis of labeled cRNA.

extract_protocol: RecoverAll™ total nucleic acid isolation kit (Ambion) or the mirVana RNA Isolation Labeling Kit (Ambion) were used. Quality control was performed with NanoDrop 2000 (Thermo Fischer Scientific) and RNA Nano 6000 chip (Agilent).

tag: disease

value: Gastric Cancer

tag: organism part

value: Stomach

value: Gastric Cancer Cell line


title: SNU-520-4


title: Animal 2, tumor 2, time 0

description:
A2T2h0
Equus caballus (ECA)
mRNA
control
processed data file: subread_processed_less_2cols_Horse_Melanoma.tsv


title: SNU-520-2


title: OmniATAC-seq_MM034_BL


title: KATOIII-3

source_name: KATOIII Cell Line

value: KATOIII


title: KATOIII-4


title: SNU-520-1


title: KATOIII-2


title: KATOIII-1


title: DLBCL111

city: Shanghai

first: Qinghhua

last: Xu

address: Cao'An Road 4800

country: China

institute: Tongji University

data_processing:
Aligner: STAR
Gene counting tool: featureCounts
Select variant calling tool: Samtools
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Lymphoid tissue

extract_protocol:
Lymph nodes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lymphoid tissue

value: Fresh frozen tissue

tag: coo subgroups


title: DLBCL110

tag: tissue

value: GCB


title: DLBCL107

value: ABC


title: AGS-4

source_name: AGS Cell Line

value: AGS


title: DLBCL109


title: DLBCL106


title: ChIP-seq_THP1_H3K27ac

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v2.2.8 with default parameters
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The bigwig files were generated using deepTools with the following argument:  bamCoverage -b input.bam -o output.bigwig -of bigwig --effectiveGenomeSize 2864785220  --normalizeUsing RPGC --ignoreDuplicates --minMappingQuality 30 --extendReads 200
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file

source_name: Human THP1 cells

growth_protocol: All the leukemia cells were cultured in RPMI supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

value: THP1 cells

tag: chip antibody


title: DLBCL108


title: ChIP-seq_U937_H3K27ac

source_name: Human U937 cells

value: U937 cells


title: DLBCL105


title: DLBCL103


title: ChIP-seq_MV4-11_H3K27ac

source_name: Human MV4-11 cells

value: MV4-11 cells


title: DLBCL104


title: DLBCL102


title: ChIP-seq_MKPL-1_H3K27ac

source_name: Human MKPL-1 cells

value: MKPL-1 cells


title: DLBCL101


title: DLBCL100


title: ChIP-seq_K562_H3K27ac

source_name: Human K562 cells

value: K562 cells


title: DLBCL099


title: AGS-1


title: AGS-3


title: YCC-3-4

source_name: YCC-3 Cell Line


title: AGS-2


title: DLBCL098


title: YCC-3-3


title: ChIP-seq_HL60_H3K27ac

source_name: Human HL60 cells

value: HL60 cells


title: YCC-6-4

source_name: YCC-6 Cell Line


title: DLBCL097


title: ChIP-seq_MKPL-1_RXRA

value: Santa Cruz, sc-515928, Lot # F2217


title: DLBCL095


title: DLBCL094


title: DLBCL092


title: DLBCL090


title: DLBCL096


title: DLBCL091


title: ChIP-seq_MKPL-1_PPARG

value: Santa Cruz, sc-271392, Lot # D1918


title: DLBCL093


title: ATAC-seq_U937

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
The bigwig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

growth_protocol: Human leukemia cell lines were cultured in RPMI supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.


title: DLBCL088


title: ATAC-seq_NB4

source_name: Human NB4 cells

value: NB4 cells


title: DLBCL089


title: DLBCL087


title: ATAC-seq_MKPL-1


title: DLBCL086


title: ATAC-seq_K562


title: DLBCL085


title: YCC-9-4

source_name: YCC-9 Cell Line

value: Gastric Cancer

value: Stomach


title: SNU-719-4

source_name: SNU-719 Cell Line

value: Gastric Cancer Cell line


title: YCC-1-4

source_name: YCC-1 Cell Line


title: DLBCL083

value: Lymphoid tissue


title: YCC-1-3


title: MKN-74-4

source_name: MKN-74 Cell Line


title: 4864N

data_processing:
Library strategy: Targeted enhancer resequencing
The adaptor and low quality bases (quality < 20) were trimmed using trim_galore version 0.4.0 with parameter --stringency 1 -e 0.1 --length 20.
Bowtie version 2.1.078 was used to align the read pairs for each sample.
PCR duplications were marked using customized pipeline.
RealignerTargetCreator/IndelRealigner from The Genome Analysis Toolkit (GATK version 3.3)18 were used to realign the reads around insertions and deletions. BaseRecalibrator/PrintReads from GATK were used to perform base quality score recalibration.
Mutations were called by the following algorithms: GATK, MuTect, Strelka, Scalpel and VarScan2.
Genome_build: hg19
Supplementary_files_format_and_content: TXT format

source_name: Normal cell

extract_protocol: Targeted resequencing of enhancer elements was performed using Ovation® Target Enrichment System (NuGEN) following the manufacture’s protocols. Target enriched library were purified, quantified, and sequenced on an Illumina NextSeq500 system using the 150bp high output sequencing kit

value: Blood cells

value: Normal cell


title: DLBCL082

value: Fresh frozen tissue

value: GCB


title: ATAC-seq_MV4-11


title: DLBCL081

value: ABC


title: 4861N


title: 4799N


title: DLBCL080


title: DLBCL084


title: 4715N


title: YCC-1-2


title: DLBCL079


title: YCC-1-1


title: YCC-11-3

source_name: YCC-11 Cell Line


title: DLBCL078

source_name: Lymphoid tissue


title: 4535N


title: YCC-11-2


title: 4696N


title: BovineMammaryEpithelialCells_12h_LPS_stimulation_rep1

city: Sendai

first: Haruki

last: Kitazawa

state: Miyagi

address: 468-1 Aramaki Aza Aoba, Aoba-ku,, Sendai

country: Japan

institute: Tohoku University

description: E. coli mastitis

hyb_protocol: The Gene Expression Hybridization kit (Agilent Technologies) was used for hybridization. In brief, 1650 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Bovine (V2) Gene Expression Microarray, 4x44K  (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 023647_D_F_20170629) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Bos taurus

source_name: Bovine mammary epithlial cells, 12hr with LPS stimulation, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini spin column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Bovine mammary epithelial cell (bMEC) line was originally established by our group (19). bMECs was derived from mammary gland tissue taken from a 200-days pregnant Holstein cows. Cells were maintained in Dulbecco’s modified Eagle medium (DMEM, Gibco, Paisley, Scotland, UK) supplemented with 20% fetal calf serum (FCS; Sigma-Aldrich, Tokyo, Japan), 100 U/ml penicillin and 100 g/ml streptomycin (Gibco 15140122, Life Technologies), transferrin (5 mg/ml) and sodium acetate (5 mM) as a growth medium. The bMEC cells were plated 2.5 ×105 /cm2 in the six-well cell culture plates (BD Falcon, Tokyo, Japan), and incubated at 37°C in a humidified atmosphere of 5% CO2. The cell culture medium was changed at every 24 h.

extract_protocol: Total RNA was extracted from the treated and untreated control cells using PureLink RNA Mini Kit (Life Technology INC., USA) along with on-column DNase treatment. RNA integrity, quality and quantity were evaluated with microcapillary electrophoresis (2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). Samples with RNA integrity number (RIN) greater than 9 were used for microarray study.

treatment_protocol: Four days-confluent bMEC cells were stimulated with LPS (0.1 µg/ml) and S. aureus JE02 (2.5 ×105 cells/well) or S. aureus SA003 (2.5 ×105 cells/well). The cultures were maintained at 37°C in a humidified atmosphere of 5% CO2 for 12 h and then harvested for RNA extraction.

value: bMEC

value: mammary epithlial cells

tag: stimulation

value: LPS


title: BovineMammaryEpithelialCells_12h_S aureus JE2_stimulation_rep1

description: S. aureus JE2 mastitis

source_name: Bovine mammary epithlial cells, 12hr with S aureus JE2 stimulation, replicate 1

value: S aureus JE2


title: 4528N


title: YCC-3-2


title: DLBCL077


title: YCC-11-4


title: 4467N


title: DLBCL076


title: BovineMammaryEpithelialCells_12h_S aureus SA003_stimulation_rep1

description: S. aureus SA003 mastitis

source_name: Bovine mammary epithlial cells, 12hr with S aureus SA003 stimulation, replicate 1

value: S aureus SA003


title: BovineMammaryEpithelialCells_12h_Without_stimulation_rep1

description: Control

source_name: Bovine mammary epithlial cells, 12hr without stimulation, replicate 1


title: DLBCL075


title: YCC-11-1


title: DLBCL074


title: 4404N


title: 4363N


title: YCC-3-1


title: DLBCL073


title: 30D.1: Human cumulus cells (CCs) cells at 30 day of culture

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

country: Poland

institute: Poznań University of Medical Sciences

description: Gene expression data from human cumulus cells (CCs) cells at 30 day of culture

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to the Affymetrix® Human Genome U219 Array (48°C/20 h). Microarrays were then washed and stained according to the technical protocol using the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: The array strips were scanned employing Imaging Station of the GeneAtlas System.

data_processing: Obtained cell files were submied to bioconductor and R programing lenguage. Each CEL file was merged with a description file.  In order to correct background, normalize, and summarize results, we used the Robust Multiarray Averaging (RMA) algorithm.

source_name: infertile female patients (range 25-40) undergoing IVF-ICSI procedure

label_protocol: Biotin labeling and fragmentation were performed by Affymetrix GeneChip® WT Terminal Labeling and Hybridization (Affymetrix).

growth_protocol: In this study we used CCs from 12 patients, aged 25-40 years, assigned to the procedure of in vitro fertilization (IVF-ICSI). The exclusion criteria from the study have been: a potential risk of inadequate ovarian stimulation; patients with serum level of FSH above 15 mU / mL on the 2nd-3rd day of the cycle; polycystic ovary syndrome; endometriosis.

extract_protocol: For reverse transcription, 1 µg of each RNA sample was used. Reverse transcription was based on the protocols and reagents of SABiosciences (RT2 First Stand Kit - 330401), using a Veritimer 96 well Thermal Cycler. Real-time PCR was performed using the Light Cycler® 96 (Roche Diagnostic GmbH, Germany), RT2 SYBR® Green ROXTM qPCR Master Mix (Qiagen Sciences, Maryland, USA)

treatment_protocol: CCs was washed twice using Dulbecco’s Phosphate Buffered Saline  (DPBS, Sigma-Aldrich, USA), and centrifugation at 200 x g for 10 min at RT. The culture medium consisted of Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma-Aldrich, USA), 2% fetal bovine serum FBS (FBS; Sigma-Aldrich Co., St. Louis, MO, USA), 4 mM L-glutamine (stock 200 mM, Invitrogen, USA), 10 mg/mL gentamicin (Invitrogen, USA), 10,000 units/mL penicillin, and 10,000 μg/mL streptomycin (Invitrogen, USA). GCs were cultivated at 37° C under aerobic conditions (5% CO2). GCs were cultivated for 30 days; total RNA was isolated after 1 day, 7 days, 15 days and 30 days.

tag: gender

value: female

value: Human cumulus cells (CCs)


title: 15D.2: Human cumulus cells (CCs) cells at 15 day of culture

description: Gene expression data from human cumulus cells (CCs) cells at 15 day of culture


title: SNU-620-3

source_name: SNU-620 Cell line


title: SNU-620-4


title: DLBCL072


title: SNU-620-1


title: 4293N


title: 30D.2: Human cumulus cells (CCs) cells at 30 day of culture


title: 15D.1: Human cumulus cells (CCs) cells at 15 day of culture


title: DLBCL071


title: SNU-620-2


title: 4274N


title: 7D.2: Human cumulus cells (CCs) cells at 7 day of culture

description: Gene expression data from human cumulus cells (CCs) cells at 7 day of culture


title: mobilized peripheral blood CD34+ cells [mPB_HD_3]

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using STAR and gene abundance estimation using featurecounts
Differential gene expression computed using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file, output of featurecounts

source_name: peripheral blood

growth_protocol: uncultured

extract_protocol:
Total RNA of CD34+ cells was extracted using ReliaPrep RNA Cell Miniprep System (Promega)
SMART-Seq v4 Ultra low-input RNA kit for sequencing (Takara Bio)

value: day 0 (uncultured)

value: mobilized peripheral blood CD34+ cells


title: 4233N


title: DLBCL070


title: mobilized peripheral blood CD34+ cells [mPB_HD_2_R]


title: SNU-601-4

source_name: SNU-601 Cell line

value: Gastric Cancer

value: Stomach


title: DLBCL069

value: Lymphoid tissue


title: 4229N

value: Blood cells


title: mobilized peripheral blood CD34+ cells [mPB_HD_1_DS]


title: DLBCL068


title: Cord blood CD34+ cells [CB7_day_0]

source_name: cord blood

value: Cord blood CD34+ cells


title: DLBCL067

value: Fresh frozen tissue


title: 24H.2: Human cumulus cells (CCs) at 24h of culture

description: Gene expression data from human cumulus cells (CCs) cells at 24h of culture


title: Cord blood CD34+ cells [CB3_day_0]


title: 7D.1: Human cumulus cells (CCs) cells at 7 day of culture


title: 24H.1: Human cumulus cells (CCs) at 24h of culture


title: 4143N

value: Normal cell


title: DLBCL066

value: GCB


title: SNU-601-2

value: Gastric Cancer Cell line


title: SNU-601-3


title: YCC-7-4

source_name: YCC-7 Cell Line


title: 3938N


title: SNU-601-1


title: Cord blood CD34+ cells [CB2_day_0]


title: 3966N


title: SNU-1-4

source_name: SNU-1 Cell Line


title: 3678N


title: CD34+ cells isolated from peripheral blood of TCIRG1-mutated patient [ARO25]


title: CD34+ cells isolated from peripheral blood of TCIRG1-mutated patient [ARO21]


title: 3644N


title: 4212N


title: DLBCL065

value: ABC


title: DLBCL064


title: SNU-216-4

source_name: SNU-216 Cell Line


title: DLBCL063


title: 3496N


title: 3491N


title: DLBCL061


title: 3450N


title: CD34+ cells isolated from peripheral blood of TCIRG1-mutated patient [ARO18]


title: DLBCL060


title: SNU-638-4

source_name: SNU-638 Cell Line


title: CD34+ cells isolated from peripheral blood of TCIRG1-mutated patient [ARO17]


title: SNU-668-4

source_name: SNU-668 Cell Line


title: MKN-1-4

source_name: MKN-1 Cell Line


title: SNU-5-4

source_name: SNU-5 Cell Line


title: 3373N

source_name: Normal cell


title: SNU-484-4

source_name: SNU-484 Cell Line


title: DLBCL059

source_name: Lymphoid tissue


title: NCI-N87-4

source_name: NCI-N87 Cell Line


title: 3348N


title: CD34+ cells isolated from peripheral blood of TCIRG1-mutated patient [ARO20]


title: DLBCL062


title: DLBCL058


title: 3255N


title: CD34+ cells isolated from peripheral blood of TCIRG1-mutated patient [ARO19]


title: DLBCL057


title: MKN-28-4

source_name: MKN-28 Cell Line


title: 3236N


title: DLBCL056


title: SNU-16-4

source_name: SNU-16 Cell Line


title: DLBCL055


title: 3230N


title: MKN-45-4

source_name: MKN-45 Cell Line


title: 2990N


title: DLBCL054


title: WSU-DLCL2

source_name: Leukemia cell line

value: Leukemia cell line


title: DLBCL053


title: U937


title: DLBCL052


title: SNU-484-3


title: DLBCL051


title: Crizotinib-sensitive_U87

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from crizotinib-sensitive U87 glioblastoma cells.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).

source_name: U87 glioblastoma cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: All the U87 cells were cultured in 10%FBS/DMEM medium, in 37 degree 5% CO2 incubator.

extract_protocol: RNAs of the U87 cells in different culture medim were collected and extracted at the same time with RNeasy Mini Kit (Qiagen Cat No./ID: 74104).

treatment_protocol: MS_E2_U87_Crizo2_24h: U87 cells cultured in 10% FBS/DMEM with 2 uM Crizotinib for 24 hours; U87_Ctr4CG_24h: U87 cells cultured in 10% FBS/DMEM without drugs for 24 hours. MS_E4_U87_CrizoR_4CR: U87 cells cultured in 10% FBS/DMEM with 1 uM Crizotinib for 21 days; MS_E4_U87_CrizoR_4CR: same growth condition to MS_E4_U87_CrizoR_4CR, just without Crizotinib.

value: glioblastoma

tag: group

value: crizotinib-sensitive


title: U266B1


title: U2932


title: SNU-484-2


title: DLBCL050


title: SNU-484-1


title: Toledo


title: Crizotinib treated_U87

description: Gene expression data from U87 glioblastoma cells treated with crizotinib for 24h.

value: 24h crizotinib


title: DLBCL049


title: Crizotinib-resistant_U87

description: Gene expression data from crizotinib-resistant U87 glioblastoma cells.

value: crizotinib-resistant


title: Vehicle_U87

description: Gene expression data from U87 glioblastoma cells treated with vehicle for 24h.

value: 24h vehicle


title: 15_7E_miR_100 precursor

city: yufu city

first: yoko

last: aoyagi

address: 1-1 Idaigaoka hamasamachi

institute: oita university

description: mRNA expression in NESCs transfected precursor hsa-miR-100

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Proliferative phase normal endometrium

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) .

treatment_protocol: Normal endometrial tissuess were obtained from premenopausal patients (n=4) who had undergone hysterectomies for leiomyoma and had no evidence of endometriosis. NESCs were isolated from the corresponding tissues by enzymatic digestion, and cultured in DMEM supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% charcoal-stripped heat-inactivated fetal FBS at 37°C in 5% CO2 in air.

value: Female

tag: age


title: 15_10E_negative control

description: mRNA expression in NESCs transfected negative control precursor


title: THP-1


title: 15_10E_miR_100 precursor


title: DLBCL048


title: NCI-N87-2

value: Gastric Cancer


title: MKN-28-3

value: Stomach


title: 15_6E_miR_100 precursor


title: NCI-N87-1


title: MKN-28-1


title: MKN-28-2


title: 15_6E_negative control


title: DLBCL047

value: Lymphoid tissue


title: SU-DHL-6

value: Blood cells


title: SU-DHL-10


title: SU-DHL-4


title: DLBCL046


title: DLBCL045


title: MKN-1-2


title: DLBCL044


title: NCI-N87-3


title: REH


title: MKN-1-3


title: DLBCL043


title: DLBCL042


title: ABC-3

city: Bunkyo-ku

first: Ayako

last: Arai

state: Tokyo

address: 1-5-45 Yushima

department: Graduate School of Medical and Dental Sciences

institute: Tokyo Medical and Dental University

hyb_protocol: The labeled cDNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

source_name: lymphnode upon dignosis

label_protocol: Total RNA were used for amplification with Ovation® RNA Amplification System V2 (NuGEN Technologies, San Carlos, CA). The Amplified cDNA were labeled by using Genomic DNA Enzymatic Labeling Kit (Agilent technologies, Santa Clara, CA). The amplification and labeling reaction were carried out according to the manufacturer’s instructions.

extract_protocol: The total RNA was purified from cells using RNeasy according to the manufacturer's instructions.

treatment_protocol: The vitreous fluid was obtained from patients of primary vitreoretinal lymphoma.

value: lymphnode

value: female

tag: diagnosis

value: diffuse large B-cell lymphoma (DLBCL)


title: Raji

tag: cell type


title: YCC-7-3

source_name: YCC-7 Cell Line


title: ABC-1

value: male


title: DLBCL041

value: Fresh frozen tissue

value: GCB


title: 14_51E_negative control


title: DLBCL040


title: Ri-1

value: Leukemia cell line


title: MKN-1-1

value: Gastric Cancer Cell line


title: YCC-7-2


title: OCI-LY7


title: RCH-ACV


title: ABC-2


title: 15_7E_negative control


title: DLBCL039


title: GCB-2


title: GCB-6


title: YCC-6-3

source_name: YCC-6 Cell Line


title: OCI-LY3


title: GCB-4


title: YCC-7-1


title: YCC-6-2


title: SNU-216-3

source_name: SNU-216 Cell Line


title: YCC-6-1


title: DLBCL038


title: ABC-4


title: NB4


title: Pfeiffer


title: GCB-5


title: DLBCL037

value: ABC


title: SNU-216-2


title: MV-4-11


title: Loucy


title: DLBCL035


title: DLBCL033


title: DLBCL034


title: Karpas


title: DLBCL036


title: PRVL-7

source_name: vitreous upon dignosis

value: vitreous

value: primary vitreo retinal lymphoma (PVRL)


title: GCB-1


title: DLBCL032


title: SNU-216-1


title: SNU-638-2

source_name: SNU-638 Cell Line


title: SNU-638-3


title: Jurkat


title: DLBCL031


title: PRVL-5


title: PRVL-6


title: SNU-638-1


title: HuT78


title: K562


title: Kasumi-2


title: DLBCL030


title: HL60


title: GDM1


title: DLBCL028


title: MKN-45-3


title: PRVL-1


title: Farage


title: SNU-5-2

source_name: SNU-5 Cell Line


title: DLBCL027


title: PRVL-3


title: PRVL-2


title: Ctrl-17


title: GCB-3


title: CD34-HSPC-2015


title: MKN-45-1


title: DLBCL026


title: MKN-45-2


title: PRVL-4


title: SNU-5-1


title: SNU-5-3


title: BC-2


title: CD34-HSPC-2008


title: DLBCL024


title: DLBCL029


title: MKPL-1


title: DLBCL022


title: SNU-1-1

source_name: SNU-1 Cell Line


title: 4864T

source_name: Leukemia cell

value: Leukemia cell


title: MKN-74-3

source_name: MKN-74 Cell Line


title: DLBCL021

source_name: Lymphoid tissue


title: SNU-1-2


title: MKN-74-2


title: 4861T


title: 4715T


title: DLBCL017


title: DLBCL019


title: DLBCL018


title: DLBCL023


title: 4535T-CD34


title: 4799T


title: MKN-74-1


title: 4696T


title: DLBCL016


title: DLBCL015


title: 4528T-CD34


title: SNU-668-3

source_name: SNU-668 Cell Line


title: DLBCL020


title: SNU-668-2


title: YCC-9-2

source_name: YCC-9 Cell Line


title: 4528T-CD14


title: SNU-719-3

source_name: SNU-719 Cell Line


title: YCC-9-3


title: DLBCL013


title: YCC-9-1


title: 4467T


title: DLBCL011


title: DLBCL012


title: DLBCL010


title: 4409


title: 4535T-CD14


title: DLBCL014


title: 4404T


title: DLBCL009


title: SNU-719-2


title: 4363T


title: SNU-668-1


title: rice.2.m6A.seal.ip

city: Los Angeles

first: Ye

last: Wang

address: 611 Charles E Young Dr E

department: Bioinformatics

institute: UCLA

data_processing:
Library strategy: m6A-SEAL
Single-end and paired-end sequencing data were trimmed by single-end and paired-end model of cutadapt (v1.18) software respectively. Reads longer than 20 bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 (v2.1.0) software using the default parameter for single or pair-end model
Peakcalling were performed by macs2(v3.8), the enrichment fold threshold is 1, FDR threshold is 0.05.
Comparison of m6A sites from MeRIP-m6A-seq and m6A-SEAL are performed by intersectBed in BEDtools.
Peaks from input and IP samples in both MeRIP-m6A-seq and m6A-SEAL are converted to bigwig files by bamCoverage script in deepTools for visualization and analysis.
Genome_build: Human genome hg38.  Rice genome built on MSU Rice Genome Annotation (Osa1) Release 7.
Supplementary_files_format_and_content: bigwig

molecule: polyA RNA

organism: Oryza sativa

source_name: rice (Nipponbare)

growth_protocol: HEK293T cell were cultured by DMEM medium(10% FBS) and 1% Penicillin Streptomycin in 15cm dish under 37℃, 5%CO2.   Rice were cultivated in a half-strength Kiruma B solution (pH 5.6, changed every two days.) at 28℃ and 80% relative humidity for 15 days.

extract_protocol:
Total RNA was first extracted from HEK293T cells or rice tissue by Trizol reagent, The polyA RNA was then purified with oligo d(T)25 magnetic beads
PolyA RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module. A portion of fragmented RNA was reserved as m6A input sample.For MeRIP-m6A-seq,  the left RNA was incubated with anti-m6A antibody and then eluted to get the m6A IP sample. For m6A-SEAL, the left RNA was enzymatically oxidized by FTO and then conjugated with biotin by dithiothreitol under acidic aqueous solution. The biotinylated RNA are enriched by streptavidin beads and then eluted by dithiothreitol to get m6A IP sample. Both input and m6A IP samples were prepared for next-generation sequencing library by standard protocol of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.
m6A-SEAL and MeRIP-m6A-seq. Library was sequenced in PE150 model on Illumina X-Ten platform or in SR75 model on Illumina NextSeq 500 platform.

tag: cultivar

value: Nipponbare

tag: method

value: leaf


title: YCC-2-4

source_name: YCC-2 Cell Line

value: Gastric Cancer

value: Stomach


title: SNU-16-2

source_name: SNU-16 Cell Line


title: DLBCL008

value: Lymphoid tissue


title: SNU-719-1


title: SNU-16-3


title: SNU-16-1


title: 4459

value: Blood cells


title: 4358


title: rice.1.m6A.seal.input


title: DLBCL007


title: 4293T


title: rice.1.m6A.seal.ip


title: rice.2.m6A.seal.input


title: YCC-2-3


title: SNU-1-3


title: KO-850

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mus musculus

source_name: Colon

extract_protocol:
Colons (0.5 cm in length, 0.5-1cm away from the anus) were removed, split open,  washed with PBS, immersed and homogeneized in 2 ml TRIzol, and toral RNA was harvested. Oligo dT was used to purify poly(A) mRNA which was subsequently reverse-transcibed into cDNA for libary construction and Illumina TruSeq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: colon

tag: treatment

value: 2.5% DSS treated for 5 days followed by two-day normal water

value: 8 weeks

tag: genotype


title: DLBCL005

tag: tissue type

value: Fresh frozen tissue


title: 4274T


title: KO-826


title: 4267


title: DLBCL004


title: 14_51E_miR_100 precursor

source_name: Proliferative phase normal endometrium

value: Female


title: YCC-2-2

tag: disease

tag: cell line


title: WT-139


title: DLBCL006

tag: coo subgroups

value: GCB


title: 4233T

tag: tissue


title: DLBCL003


title: WT-140


title: 4245T


title: YCC-2-1

tag: organism part

value: Gastric Cancer Cell line


title: YCC-16-4

source_name: YCC-16 Cell Line


title: DLBCL002

value: ABC


title: DLBCL025


title: 4229T


title: DLBCL001


title: 4212T


title: Donor 4 CD26+ CD94lo +IL2 (D4 26 IL2)

description:
Sample 27
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

data_processing:
RNAseq analysis was performed using the web-based Galaxy platform maintained by Galaxy Australia.
Reads were mapped to the Homo sapiens reference genome (hg38) using HISAT2 and reads were quantified using HTSeq.
Count matrices were generated and inputted into Degust (http://degust.erc.monash.edu) for final data analysis and visualization. The Degust Voom/Limma method was selected for data processing.
Genome_build: hg38
Supplementary_files_format_and_content: CSV/tab-delimited text files include raw counts or CPM values
Supplementary_files_format_and_content: Degust_Voom_Limma - IL23 expansion.csv: Normalized abundance measurements - Degust output
Supplementary_files_format_and_content: Raw counts - IL23 expansion.txt: Raw counts - Htseq

source_name: Human PBMC

extract_protocol:
RNA was isolated from sorted cells using a Zymo Direct-zol RNA MicroPrep Kit, as per manufacturer's protocol.
Illumina Truseq Stranded mRNA kit was use for library construction. RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC

value: CD3+ Vd2+ CD26+ CD94lo +IL2


title: EtOH-rep2

city: Ames

first: Andrew

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

description: Mosquito cell lines were exposed to 10% ethanol (control).

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were quality checked with fastqc, mapped to Agam 4.7 whole genome using STAR v2.5.2b.
FeatureCounts from subread was used to estimate read counts for genes.
Genome_build: AgamP4.7
Supplementary_files_format_and_content: counts_genes_EtOH_20E.txt: Tab-delimited text file includes raw counts for each Sample.

organism: Anopheles gambiae

source_name: Sua 4.0 cells

extract_protocol:
Following cell treatments, cells were incubated for 24 hours before control- and 20E-treated cell samples were isolated. RNA was isolated using TRIzol reagent and evaluated for quality using an Agilent 2100 Bioanalyzer. Samples were sent to the DNA Facility at Iowa State University for library construction and stranded mRNA-Seq. Gene expression analysis was performed the Genome Informatics Facility at Iowa State University.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mosquito cell lines were exposed to 10% ethanol (control) or 20-hydroxyecdysone (20E) in 10% ethanol for 24 hrs.

value: Sua 4.0

value: control


title: 4143T

value: Leukemia cell


title: Donor 5 CD26+ CD94lo +IL2 (D5 26 IL2)

description:
Sample 28
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt


title: EtOH-rep1


title: EtOH-rep3


title: EtOH-rep4


title: YCC-16-2

value: Gastric Cancer


title: YCC-16-1

value: Stomach


title: Hs746T-4

source_name: Hs746T Cell Line


title: 4009


title: Donor 5 CD26+ CD94lo +IL2 +IL23 (D5 26 IL2 IL23)

description:
Sample 26
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26+ CD94lo +IL2 +IL23


title: Hs746T-3


title: YCC-16-3


title: Hs746T-2


title: 3966T

value: Blood cells


title: 20E-Rep4

description: Mosquito cell lines were exposed to 20-hydroxyecdysone (20E) in 10% ethanol.

value: 20-hydroxyecdysone (20E)


title: 20E-Rep3


title: GOX_AGXX30_GA

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: GOX_AGXX T30_GA

data_processing:
mapping of reads was done using: bowtie2  --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Staphylococcus aureus 04-02981|VERSION Date:   2010/11/05 | ASM2514v1 | GenBank assembly accession: GCA_000025145.2
Supplementary_files_format_and_content: counts (text tab delimited table)

organism: Staphylococcus aureus

source_name: human

growth_protocol: Bacterial cells were grown in Tryptic Soy Broth at 37°C, 150 rpm shaking

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation protocol of BGI for Illumina RNA-Seq

treatment_protocol: The bacterial culture was exposed to either uncoated cellulose fibers or GOX fibers (coated on cellulose) or AGXX® fibers (coated on cellulose) or GOX+AGXX® fibers, the culture without addition of any antimicrobial fibers served as the control

tag: time

value: 30 min


title: Donor 5 CD26- CD94hi +IL2 (D5 94 IL2)

first: Hyon Xhi

address: 792 Elizabeth St

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

description:
Sample 24
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26- CD94hi +IL2


title: GOX_AGXX60_GA

description: GOX_AGXX T60_GA

value: 60 min


title: Donor 5 CD26+ CD94hi +IL2 +IL23 (D5 DP IL2 IL23)

description:
Sample 23
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26+ CD94hi +IL2 +IL23


title: GOX_AGXX180_GA

description: GOX_AGXX T180_GA

value: 180 min


title: Hs746T-1

value: Gastric Cancer Cell line


title: GOX_AGXX120_GA

description: GOX_AGXX T120_GA

value: 120 min


title: Donor 5 CD26- CD94hi +IL2 +IL23 (D5 94 IL2 IL23)

description:
Sample 25
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: PBMC

value: CD3+ Vd2+ CD26- CD94hi +IL2 +IL23


title: 3749


title: 3753


title: 20E-Rep2

value: Sua 4.0


title: 3938T


title: Donor 5 CD26+ CD94hi +IL2 (D5 DP IL2)

description:
Sample 21
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26+ CD94hi +IL2


title: Donor 5 CD26- CD94lo +IL2 +IL23 (D5 DN IL2 IL23)

description:
Sample 22
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26- CD94lo +IL2 +IL23


title: 20E-Rep1


title: 3710

value: Leukemia cell


title: GOX_AGXX0_GA

description: GOX_AGXX T0_GA

value: 0 min


title: 3953T


title: Donor 5 CD26- CD94lo +IL2 (D5 DN IL2)

description:
Sample 20
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26- CD94lo +IL2


title: GOX30

description: GOX T30

value: GOX


title: Donor 4 CD26+ CD94lo +IL2 +IL23 (D4 26 IL2 IL23)

description:
Sample 19
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26+ CD94lo +IL2 +IL23


title: Donor 4 CD26- CD94hi +IL2 +IL23 (D4 94 IL2 IL23)

description:
Sample 18
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt


title: 3678T

value: Blood cells


title: 3644T


title: GOX180

description: GOX T180


title: GOX120

description: GOX T120


title: 3624


title: Donor 4 CD26+ CD94hi +IL2 (D1 DP IL2)

description:
Sample 14
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt


title: 3496T-MDS


title: 3373T


title: Donor 4 CD26- CD94lo +IL2 +IL23 (D4 DN IL2 IL23)

description:
Sample 15
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt


title: Control120_C

description: Control T120_C

value: Control


title: Control0_C

description: Control T0_C


title: Donor 4 CD26- CD94hi +IL2 (D4 94 IL2)

description:
Sample 17
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26- CD94hi +IL2


title: GOX0

description: GOX T0


title: Control180_C

description: Control T180_C


title: 3491T


title: 3450T


title: 3365


title: Control60_C

description: Control T60_C

value: 60 min


title: Donor 4 CD26+ CD94hi +IL2 +IL23 (D4 DP IL2 IL23)

description:
Sample 16
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: CD3+ Vd2+ CD26+ CD94hi +IL2 +IL23


title: Secondary3_D1

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v2.1.1 mkfastq pipline (10x Genomics) and bcl2fastq2 v 2.20.0 (Illumina)
Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v2.1.1 count pipeline (10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, mtx files generated by CellRanger v2.1.1

source_name: Sorted PBMC

extract_protocol:
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics) according to the manufacture's protocol (User guide RevC)
Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol (User guide RevC). In short, sequencing libraries were generated by  1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: Cryopreserved PBMCs were thawed and washed with RPMI media supplemented with 10% fetal calf serum prior to analysis. Populations of interest (CD3+CD19- T cells and CD3-CD19+ B cells) were isolated from the unfractionated PBMCs by flow cytometric sorting using a BD FACSAria Fusion instrument. Post-sort population purity was assessed prior to downstream analysis, and sorted T and B cells pooled together in for subsequent processing. Sorted cells were washed in PBS supplemented with 2% fetal calf serum prior to scRNAseq library generation

tag: patient diagnosis

value: natural secondary DENV infection

value: Pooled CD3+CD19- T cells and CD3-CD19+ B cells

tag: subject

value: Secondary #3

tag: fever day

value: Fever day 1


title: Donor 4 CD26- CD94lo +IL2 (D4 DN IL2)

city: Melbourne

last: Tan

description:
Sample 13
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt

value: PBMC


title: Cellulose60_Cell

description: Cellulose T60_Cell

value: Cellulose


title: Cellulose30_Cell

description: Cellulose T30_Cell

value: 30 min


title: C149 (TCR-seq)

city: Shenzhen

first: Zheng

last: Zhang

state: Guangdong

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

description: TCRseq data

data_processing:
Library strategy: TCR-seq
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell 5’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically. Finally, gene-barcode matrix of all 12 donors and 1 previously reported healthy control was integrated with Seurat v3 to remove batch effect across different donors. Following criteria were then applied to each cell, i.e., gene number between 200 and 6000, UMI count above 1000 and mitochondrial gene percentage below 0.1.
The filtered gene-barcode matrix was normalized with LogNormalize methods in Seurat and analyzed by principal component analysis (PCA) using the top 2, 000 most variable genes. Then Uniform Manifold Approximation and Projection (UMAP) was performed on the top 50 principal components for visualizing the cells. Meanwhile, graph-based clustering was performed on the PCA-reduced data for clustering analysis with Seurat v3.
MAST in Seurat v3 was used to perform differential analysis. For each cluster, differentially-expressed genes (DEGs) were generated relative to all of the other cells.
The TCR sequences for each single T cell were assembled by Cell Ranger vdj pipeline (v3.1.0), leading to the identification of CDR3 sequence and the rearranged TCR gene. Cells with both TCR alpha and beta chains were kept and cells with only one TCR chain were discarded.
Genome_build: GRCh38 + COVID(MN908947)
Supplementary_files_format_and_content: h5, raw count matrix generated by Cell Ranger count; csv, tcr contig annotations generated by Cell Ranger vdj

source_name: BALF

extract_protocol: Total 11 µl of single cell suspension and 40 µl barcoded Gel Beads were loaded to Chromium Chip A to generate single-cell gel bead-in-emulsion (GEM). The poly-adenylated transcripts were reverse-transcribed later. The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 5’ library preparation kit according to the manufacturer’s protocol (10x Genomics). Full-length cDNA along with cell-barcode identifiers were PCR-amplified and sequencing libraries were prepared and normalized to 3 nM.

tag: patient group

value: severe COVID-19 patient

value: lung

tag: sample type

value: bronchoalveolar lavage fluid (BALF)

tag: cell subsets

value: Total cell


title: C152 (TCR-seq)

description: TCRseq data


title: Secondary3_D0

tag: cell type

value: Fever day 0


title: C148 (TCR-seq)

description: TCRseq data


title: 3573

source_name: Leukemia cell

value: Blood cells

value: Leukemia cell


title: 3324


title: Control30_C

description: Control T30_C

tag: strain

value: Control


title: Secondary3_D5

value: Fever day 5


title: Secondary2_D5

value: Secondary #2


title: Cellulose120_Cell

description: Cellulose T120_Cell

tag: treatment

value: 120 min


title: 3279


title: Cellulose0_Cell

description: Cellulose T0_Cell

value: 0 min


title: Secondary2_D1

value: natural secondary DENV infection

value: Pooled CD3+CD19- T cells and CD3-CD19+ B cells


title: C149 (scRNA-seq)

description: Single-cell RNAseq

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell 5’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically. Finally, gene-barcode matrix of all 12 donors and 1 previously reported healthy control was integrated with Seurat v3 to remove batch effect across different donors. Following criteria were then applied to each cell, i.e., gene number between 200 and 6000, UMI count above 1000 and mitochondrial gene percentage below 0.1.
The filtered gene-barcode matrix was normalized with LogNormalize methods in Seurat and analyzed by principal component analysis (PCA) using the top 2, 000 most variable genes. Then Uniform Manifold Approximation and Projection (UMAP) was performed on the top 50 principal components for visualizing the cells. Meanwhile, graph-based clustering was performed on the PCA-reduced data for clustering analysis with Seurat v3.
MAST in Seurat v3 was used to perform differential analysis. For each cluster, differentially-expressed genes (DEGs) were generated relative to all of the other cells.
The TCR sequences for each single T cell were assembled by Cell Ranger vdj pipeline (v3.1.0), leading to the identification of CDR3 sequence and the rearranged TCR gene. Cells with both TCR alpha and beta chains were kept and cells with only one TCR chain were discarded.
Genome_build: GRCh38 + COVID(MN908947)
Supplementary_files_format_and_content: h5, raw count matrix generated by Cell Ranger count; csv, tcr contig annotations generated by Cell Ranger vdj


title: C152 (scRNA-seq)

description: Single-cell RNAseq


title: Cellulose180_Cell

description: Cellulose T180_Cell

value: 180 min


title: Secondary2_D-1

value: Fever day -1


title: AGXX60

description: AGXX T60

value: AGXX

value: 60 min


title: Secondary1_D1

value: Secondary #1

value: Fever day 1


title: 3236T-MDS


title: C148 (scRNA-seq)

description: Single-cell RNAseq

value: severe COVID-19 patient

value: lung

value: bronchoalveolar lavage fluid (BALF)

value: Total cell


title: 3255T

value: Blood cells

value: Leukemia cell


title: 3230T


title: C100 (scRNA-seq)

description: Single-cell RNAseq

value: healthy control


title: AGXX30

description: AGXX T30

value: 30 min


title: Secondary1_D7

value: Fever day 7


title: 3348T


title: AGXX180

description: AGXX T180


title: Secondary1_D0

value: natural secondary DENV infection

value: Fever day 0


title: 3208


title: C52 (scRNA-seq)

description: Single-cell RNAseq


title: C51 (scRNA-seq)

description: Single-cell RNAseq


title: 3175


title: Primary3_D2

value: natural primary DENV infection

value: Pooled CD3+CD19- T cells and CD3-CD19+ B cells

value: Primary #3

value: Fever day 2


title: AGXX120

description: AGXX T120

value: AGXX

value: 120 min


title: BALF, C146 (TCR-seq)

description: TCRseq data

data_processing:
Library strategy: TCR-seq
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell 5’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically. Finally, gene-barcode matrix of all 6 donors and 8 previously reported healthy control was integrated with Seurat v3 to remove batch effect across different donors. Following criteria were then applied to each cell, i.e., gene number between 200 and 6000, UMI count above 1000 and mitochondrial gene percentage below 0.1.
The filtered gene-barcode matrix was normalized with LogNormalize methods in Seurat and analyzed by principal component analysis (PCA) using the top 2, 000 most variable genes. Then Uniform Manifold Approximation and Projection (UMAP) was performed on the top 50 principal components for visualizing the cells. Meanwhile, graph-based clustering was performed on the PCA-reduced data for clustering analysis with Seurat v3.
MAST in Seurat v3 was used to perform differential analysis. For each cluster, differentially-expressed genes (DEGs) were generated relative to all of the other cells.
The TCR sequences for each single T cell were assembled by Cell Ranger vdj pipeline (v3.1.0), leading to the identification of CDR3 sequence and the rearranged TCR gene. Cells with both TCR alpha and beta chains were kept and cells with only one TCR chain were discarded.
Genome_build: GRCh38 + COVID(MN908947)
Supplementary_files_format_and_content: h5, raw count matrix generated by Cell Ranger count; csv, tcr contig annotations generated by Cell Ranger vdj

tag: disease state

value: Coronavirus infected disease-19 (COVID-19)

value: severe

tag: organ

value: BALF


title: 3173


title: AGXX0

description: AGXX T0

value: 0 min


title: 3171

value: Blood cells


title: BALF, C145 (TCR-seq)

description: TCRseq data

value: lung

value: Total cell


title: BALF, C143 (TCR-seq)

description: TCRseq data


title: Primary2_D5

value: Primary #2

value: Fever day 5