title: K562 cells, NMYB overexpression, 3

first: Yucheng

address: Huchenghuan Rd

department: College of Fisheries and Life Science

institute: Shanghai Ocean University

data_processing:
Sequence reads were adapter and quality trimmed using Trimmomatic (v 0.93).
Trimmed sequence reads were mapped to GRCh38 using Hisat2 (v 2.2.1).
Read counts were quantitated using featureCounts (v 2.0.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bone marrow

growth_protocol: K562 cells were maintained in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS).

extract_protocol:
RNAs were extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions. 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer’s protocols.

value: bone marrow

value: human erythroleukemic cells

value: NMYB overexpression


title: PIF4S344A-28_biol rep 1

status: Public on Aug 01 2024

type: SRA

city: New Delhi

first: Alok

middle: Krishna

last: Sinha

state: Delhi

address: Aruna Aasaf Ali Marg

department: National Institute of Plant Genome Research

country: India

library_source: genomic

data_processing:
Raw sequencing reads were mapped to theArabidopsis thaliana genome (TAIR10) by Bowtie2 version 2.4.2 with default parameters (Langmead and Salzberg, 2012).
Reads were normalized as reads per kilobase per million mapped reads (RPKM) in 10 bp windows using the bamCoverage tool in deepTools and visualized in Integrative Genomics Viewer (IGV). The fragment size distribution was obtained from the bamPEFragmentSize tool in deepTools (Ramirez etal., 2014).
To obtain the enrichment signal around the transcription start site (TSS), we employed computeMatrix tool in deepTools. Using the ChIPpeakAnno  package, we determined the intersection of peaks in two replicates as the final set of enriched peaks for each sample.
DiffBind was used to perform differential enrichment analysis of H2A.Z. Differentially enriched peaks with FDR ≤ 0.05 were filtered.
The differentially bound sites predicted by Diffbind were converted to gene using seq2gene. These genes were then input for KEGG and GO enrichment analysis.
Supplementary_files_format_and_content: bdg files were generated using  using Macs2 with SPMR normalization.
Assembly: TAIR10
Supplementary files format and content: bdg

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Seeds were surface-sterilized by treatment with 70% alcohol for 5 min and then washed with HgCl2, and then washed with water for 8 times. After sterilization, seeds were sown onto 1/ 2MS nutrient medium and were incubated at 4°C overnight and then in darkness for more than 3 days, followed by short-day condition (8h light and 16h dark at 22℃ and 28℃) for 10 days.

extract_protocol:
ChIP was performed as previously described (Yang et al., 2020).
The paired-end sequencing libraries were prepared from the DNA samples using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. Briefly, approximately 10ng of DNA was processed for end-repair followed by adaptor ligation as per the kit protocol. The ligated products were subjected to purification using NEBNext Sample purification beads. The purified products were PCR amplified with the index primer followed by AMPureXP bead purification. The PCR enriched libraries were analyzed on 4200 Tape Station system (Agilent Technologies) using D1000 Screen tape as per manufacturer instructions. After obtaining the Qubit concentration for the libraries and the mean peak sizes from Agilent Tape Station profile, the PE illumina libraries were loaded onto Novaseq6000 for cluster generation and sequencing.

treatment_protocol: Seedlings given ambient and elevated temperature treatments of 22 and 28℃.

tag: tissue

value: Seedling

tag: cell type

value: 10 days old seedlings

tag: antibody

tag: treatment

value: temperature treatment


title: HEK293, pSer2, T4WT, rep2

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

country: USA

institute: The University of Texas at Austin

data_processing:
After initial assessment of read quality, pSer2 and  RPRD1B (HA-tag) ChIP-Seq data was mapped onto human reference genome, hg38, with Bowtie2 v. 2.5.0 aligner for paired-end reads using default parameters. pThr4 single-end ChIP-Seq reads were mapped onto human reference genome, hg19, using BWA v.0.7.17.
Coverage tracks in .bigwig format were generated from filtered .bam files (mapq > 20).
TSS/TES profiling was done using plotProfile on matrices generated with 50-bp bins using the computeMatrix function from the deeptools v.2.2.3
After alignment, MACS2 v.2.2.7.1 in Galaxy (parameters: --broad; --broad-cutoff of q < 0.1 for pThr4 and HA-RPRD1B; pSer2 -default) was used to call peaks for IP-samples against Input.
Assembly: hg19 (pThr4), hg38 (pSer2, HA-RPRD1B)
Supplementary files format and content: bigWig, broadPeak

organism: Homo sapiens

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Briefly, for HA-tagged RPRD1B, HEK293 cells were double crosslinked with 2mM DSG for 15 min followed by secondary fixation with 1% formaldehyde for 10 min at room temperature. Single crosslinking was used for RPB1 ChIP using 1% formaldehyde for 10 min. Crosslinking was quenched with 0.125 M glycine for 5 min. Cells were successively lysed in lysis buffer LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× PI), LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× PI) and LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× PI). Chromatin was sonicated to an average size of ~200–500 bp using UCD-200 Biorupter (30s on and 30 s off for 30 min). A total of 5 μg of HA antibody (cat: C29F4), pThr4 antibody (Active Motif, cat: 61361), or pSer2 antibody (Sigma, SKU: MABE953) was pre-mixed in a 50μl volume of Dynabeads protein A or protein G (Invitrogen) and was added to each sonicated chromatin sample and incubated overnight at 4°C. The chromatin-bound beads were washed two times with low salt buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 150mM NaCl), once with high salt wash buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.0) and twice in TE buffer. The chromatin was reverse crosslinked overnight at 65°C with shaking at 750rpm. After DNA extraction using phenol-chloroform, the DNA was resuspended in 10mM Tris-HCl pH 8.0.
The extracted DNA was used to construct the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit followed by sequencing with an Illumina HiSeq 3000 or NovaSeq X Plus system.

treatment_protocol: To prepare samples for pThr4 ChIP, we treated HEK293 cell lysate with Ssu72/symplekin complex at 4°C for 30 minutes before binding to the 6D7 antibody. To generate T4A and T4WT CTD samples for pSer2 immunoprecipitation, transient transfection of 12 μg of either plasmid was performed using PEI. Following transfection, 2.5 μg of alpha amanitin was added to cells for 48 hours. Finally, to prepare HA-RPRD1B samples, HEK293 were transfected with HA-RPRD1B using PEI (1:7 plasmid to reagent ratio) to overexpress the protein of interest.

tag: cell line

value: Human embryonic kidney

tag: chip antibody

value: pSer2 (Sigma, #MABE953)


title: cardiomyocyte,TAC2w, replicate1-75, scRNAseq

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description:
smartseq2
TAC2w_1.xlsx

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

value: cardiomyocyte

value: heart

tag: strain

tag: age

value: 6-8 weeks old


title: PIF4S344A-22_biol rep 2

institute: National Institute of Plant Genome Research


title: K562 cells, NMYB overexpression, 2

city: Shanghai

last: Wang

country: China

library_source: transcriptomic

tag: genotype


title: cardiomyocyte,TAC2w, replicate1-74, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: bacteria in mineral water, day 7, replicate 1

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

data_processing:
Sequencing data was demultiplexed with bcl2fastq2 (v2.18.12, Illumina), adapters were trimmed with Cutadapt (v3.2), and only reads longer than 10bp were kept.
Alignment to the reference sequence of the L. monocytogenes EGDe (Genbank RefSeq NC_003210.1) was done using the Bowtie2 alignment tool version 2.4.4.
Stranded read counts per gene annotated in NC_003210.1 were obtained with featureCounts program included subread v2.0.1 (options “-p -Q 30 -s 2")
Relative library sizes were estimated on genes with a count of at least 5 in at least 3 out of the 6 samples using the robust estimation method implemented in DESeq2 v1.38.3.
Fragment counts normalised per kilobase of feature length per million mapped fragments (FPKM) were computed with DESeq2 based on relative library sizes.
Assembly: Genbank RefSeq NC_003210.1
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: First five columns : location of the feature on NC_003210.1, source (Genbank or Listeriomics), locus tag,
Supplementary files format and content: Next six columns : raw counts for each sample
Supplementary files format and content: Last six columns : normalized expression levels (FPKM) for each sample

organism: Listeria monocytogenes EGD-e

source_name: planktonic cells (10^8 cells/mL)

growth_protocol:
Bacteria were grown overnight to stationary phase at 37°C in brain and heart infusion (BHI) broth (with agitation).
Cells were pelleted by centrifugation (3,000×g, 3min) and washed with sterile-filtered (0.22µm) mineral water for three times before resuspension in mineral water at a concentration of 10^8 CFU/ml.
Cells suspensions in mineral water were incubated statically at room temperature in an upright-standing, sterile tissue-culture flask (25cm2, vented cap).
Samples were collected immediately after preparation (“day0”) and after 7 days.

extract_protocol:
Total RNAs were recovered from bead-beaten bacterial cells using a phenol/chloroform extraction method.
The quality of RNA extracts was assessed in an Agilent Bioanalyzer 2100, using the RNA 6000 pico kit (Agilent Technologies).
Total RNAs (450ng) were treated with DNase (Baseline-ZERO DNase, Epicentre).
Library construction -including ribosomal RNA depletion- and sequencing was performed by I2BC sequencing facility (Gif-sur-Yvette).
Ribosomal RNA was removed using the Illumina Ribo-Zero Magnetic Kit (Bacteria), according to the manufacturer recommendations.
Directional RNA sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep kit (Illumina), and library quality was assessed on an Agilent Bioanalyzer 2100, using the Agilent High Sensitivity DNA Kit (Agilent Technologies).
Libraries were pooled and sequenced in 2×75-bp paired-end runs on a NextSeq500 instrument, using a NextSeq500 High Output 150 cycles kit (Illumina).

treatment_protocol: Bacteria (10^9 cells) were harvested (5000×g, 3min) from mineral water suspensions and immediately flash-frozen in liquid nitrogen and stored at −80°C until further processing.

value: planktonic cells (10^8 cells/mL)

value: suspension in mineral water, after seven day


title: K562 cells, NMYB overexpression, 1


title: cardiomyocyte,TAC2w, replicate1-73, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: CD3+ cells,Patient 2,During (8 weeks),3

city: Cambridge

first: Eloi

last: Schmauch

state: Massachusetts

address: 32 Vassar St

department: Computer Science and Artificial Intelligence Laboratory

institute: Massachusetts Institute of Technology

description: Count matrix column name: P2_002_CD3_BEFORE

data_processing:
Raw sequencing FASTQ files are compiled with a configuration file that defines processing parameters. Adapter sequences are then computationally removed from these files, and overlapping paired-end reads are merged. The resulting reads are aligned to RTS-ID barcodes in the reference assay, with raw counts assigned to biological target names. Next, PCR duplicates are eliminated using Unique Molecular Identifiers, producing deduplicated reads. Finally, the processed data is saved as DCC files, which were then uploaded to the GeoMx DSP system for further analysis or for processing with GeomxTools in R.
dcc-metadata = false; save-interim-files = false; quality-trim-score = 20; 2color-trimming = True; adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; adapter-trim-match-length = 10; adapter-trim-max-mismatch = 3; barcode-max-mismatch = 1; stitching-max-mismatch = 2; dedup-hd = 1; threads = 4
The raw count matrix (for each ROI) was obtained with Nanostring GeoMX DSP according to the instruction manual.
Assembly: GRCh38
Supplementary files format and content: Raw counts matrix - countains counts for each gene (rows), for each ROI (columns)
Supplementary files format and content: dcc files (inputs for GeoMX DSP software)
Library strategy: Spatial Transcriptomics

source_name: skin

extract_protocol:
The RNA extraction was performed according to the protocol. The GeoMx Digital Spatial Profiler (DSP) uses nucleic acid probes coupled to photocleavable oligonucleotide tags which hybridize to targets in slide-mounted tissue sections. Via UV exposure the oligonucleotide tags are released from discrete regions of interest (ROIs) in the tissue. The UV-cleaved oligos are transferred to a collection plate for Library Pre with Seq Code primers. Later they are quantitated by Illumina Next Generation Sequencing. Results are mapped back to tissue location, yielding a spatially resolve digital profile.
Library preparation was performed according to Nanostring GeoMX NGS Manual. A specific thermocycler program is set for the PCR process, including various temperature and time settings for steps like UDG incubation, denaturation, annealing, extension, and final holding.
Preparation involves selecting the correct primer plates based on the lab worksheet, thawing them, and mixing them with the GeoMx NGS Master Mix and sample aspirates according to defined volumes. This is followed by aliquoting the master mix, transferring primers, and sample aspirates into a new PCR plate. Post-PCR, products are pooled and undergo AMPure cleanup—a bead-based method for purifying the PCR products.
The purified library's quality is assessed through capillary electrophoresis, ensuring the correct amplicon size and absence of undesirable products. Quantification of the library concentration is done using Qubit or qPCR. Finally, the library is stored at -20°C until sequencing, with recommendations provided for pooling multiple sample pools for a sequencing run and adjusting loading concentrations based on the Illumina platform used.

value: skin

tag: roi selected

value: CD3+ cells

tag: patient

value: Patient 2

value: During (8 weeks)

tag: technical sample_id


title: PIF4S344A-22_biol rep 1


title: IP_NGA_placental_4

type: RNA

city: Shenyang

first: Dan

state: Liaoning Province, China

address: No.16, Puhe Avenue, Shenbei New District

department: Department of Obstetrics and Gynecology

institute: Shengjing Hospital of China Medical University

description:
Raw data file:
NGA_4.txt
NGA placental tissue-4

hyb_protocol: The “IP” and “Sup” RNAs were treated with RNase R, and then labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit. The cRNAs were combined together and hybridized onto Arraystar Human circRNA Epitranscriptomic Microarray (8x15K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
Data was extracted using Agilent Feature Extraction software. The probe signals passing P or M QC flags in at least 3 samples were retained for further analysis.
IP (Cy5-labelled) and Sup (Cy3-labelled) intensities were normalized by the RNA spike-in calibration controls. m6A methylation levels were calculated for the percentage of modified RNA of a transcript.  IP (Cy5-labelled) intensities were normalized as relative intensities by the RNA spike-in calibration controls. The normalized IP intensities represent the m6A quantity of the transcript comparable across samples.

source_name: placental tissue

label_protocol: And the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”.

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000.

tag: gender

value: female

value: placental

tag: condition

value: normal for gestational age

tag: rip antibody

value: RNA immunoprecipitated with anti-N6-methyadenosine (m6A) antibody


title: bacteria in mineral water, day 0, replicate 3

value: suspension in mineral water, first day


title: bacteria in mineral water, day 0, replicate 2


title: K562 cells, MYB overexpression, 3

value: bone marrow

value: human erythroleukemic cells

value: MYB overexpression


title: pif4-28_biol rep 1

value: Seedling

value: 10 days old seedlings

value: temperature treatment


title: K562 cells, MYB overexpression, 2


title: cardiomyocyte,TAC2w, replicate1-72, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: pif4-28_biol rep 2


title: K562 cells, MYB overexpression, 1


title: pif4-22_biol rep 2


title: SK-N-MC, EGFPCAG78, PAPD5-siRNA treatment (rep3)

city: Hong Kong

first: Ho Yin Edwin

last: Chan

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
SK-N-MC cells transfected with EGFPCAG78 upon PAPD5-siRNA treatment
SAMPLE 18

data_processing:
The Ct values were automatically generated from the ABI QuantStudio 7 Real-time PCR System.
The Ct values from target miRNAs were normalized to the Ct value of housekeeping gene U6 snRNA (ΔCt = Cttarget miRNA – CtU6 snRNA).
The ΔCt values of hsa-let-7b-5p miRNA from three sets of “Untransfected + control-siRNA” samples were averaged to obtain the ΔCtaveraged, and Ct values from each set of control and experimental group samples were further normalized to ΔCtaveraged to obtain the ΔΔCt values (ΔΔCt = Ct – ΔCtaveraged).
Target miRNA expression was calculated using 2^-ΔΔCt method.
Matrix normalized worksheet reports normalized signal (ΔΔCt values).
Fold Change worksheet reports target miRNA expression (2^-ΔΔCt method).

label: SYBR Green

source_name: SK-N-MC, EGFPCAG78, PAPD5-siRNA

label_protocol: PCR assays were performed using the Qiagen miRCURY LNA miRNA miRNome PCR Panel following the Manufacturer’s instructions. Reverse transcription was performed using miRCURY® LNA® RT system (Qiagen). Quantitative real-time PCR were performed (QuantStudio 7, ABI) with 45 cycles at 95 °C for 15 seconds and 60 °C for 60 seconds.

growth_protocol: The human neuroblastoma SK-N-MC cells (HTB-10TM, American Type Culture Collection) were cultured in DMEM (11995065, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (F7524, Sigma-Aldrich) and 1% penicillin–streptomycin (15140122, Thermo Fisher Scientific).

extract_protocol: Small RNA species from SK-N-MC cells were purified using RNeasy Mini (Qiagen) and RNeasy MinElute Cleanup (Qiagen) kits.

treatment_protocol: Plasmid DNA and siRNA transfection was performed using Lipofectamine 2000 (11668019, Thermo Fisher Scientific) and Lipofectamine RNAiMAX (13778150, Thermo Fisher Scientific), respectively.

value: Human neuroblastoma cell line SK-N-MC

tag: plasmids used

tag: sirnas used


title: cardiomyocyte,TAC2w, replicate1-71, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

tag: tissue


title: bacteria in mineral water, day 0, replicate 1

tag: cell type

value: planktonic cells (10^8 cells/mL)


title: cardiomyocyte,TAC2w, replicate1-70, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: SK-N-MC, EGFPCAG78, control-siRNA treatment (rep3)

description:
SK-N-MC cells transfected with EGFPCAG78 upon scramble control siRNA treatment
SAMPLE 17

source_name: SK-N-MC, EGFPCAG78, control-siRNA

value: control-siRNA


title: pif4-22_biol rep 1

tag: antibody


title: K562 cells, empty vector, 3

value: empty vector


title: SK-N-MC, EGFPCAG27, PAPD5-siRNA treatment (rep3)

description:
SK-N-MC cells transfected with EGFPCAG27 upon PAPD5-siRNA treatment
SAMPLE 16

source_name: SK-N-MC, EGFPCAG27, PAPD5-siRNA


title: K562 cells, empty vector, 2


title: arp6-28_biol rep 2

tag: treatment


title: cardiomyocyte,TAC2w, replicate1-68, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: arp6-28_biol rep 1


title: SK-N-MC, EGFPCAG27, control-siRNA treatment (rep3)

description:
SK-N-MC cells transfected with EGFPCAG27 upon scramble control siRNA treatment
SAMPLE 15

source_name: SK-N-MC, EGFPCAG27, control-siRNA

tag: cell line


title: K562 cells, empty vector, 1


title: SK-N-MC, Untransfected, PAPD5-siRNA treatment (rep3)

description:
SK-N-MC cells untransfected control upon PAPD5-siRNA treatment
SAMPLE 14

source_name: SK-N-MC, Untransfected, PAPD5-siRNA


title: arp6-22_biol rep 2


title: cardiomyocyte,TAC2w, replicate1-67, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: K562 cells, 34kp, 3

data_processing:
Sequence reads were adapter and quality trimmed using Trimmomatic (v 0.93).
Trimmed sequence reads were mapped to GRCh38 using STAR (2.7.10a).
Differential exon usage analysis was done with DEXSeq package (1.20.2).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene exon bin counts for each sample


title: cardiomyocyte,TAC2w, replicate1-66, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: arp6-22_biol rep 1


title: SK-N-MC, Untransfected, control-siRNA treatment (rep3)

description:
SK-N-MC cells untransfected control upon scramble control siRNA treatment
SAMPLE 13

source_name: SK-N-MC, Untransfected, control-siRNA


title: K562 cells, 34kp, 2


title: cardiomyocyte,TAC2w, replicate1-65, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: SK-N-MC, EGFPCAG78, PAPD5-siRNA treatment (rep2)

description:
SK-N-MC cells transfected with EGFPCAG78 upon PAPD5-siRNA treatment
SAMPLE 12


title: WT-28_biol rep 2


title: K562 cells, 34kp, 1


title: cardiomyocyte,TAC2w, replicate1-64, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: cardiomyocyte,TAC2w, replicate1-69, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: K562 cells, 34kpContol, 3


title: cardiomyocyte,TAC2w, replicate1-63, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: SK-N-MC, EGFPCAG27, PAPD5-siRNA treatment (rep2)

description:
SK-N-MC cells transfected with EGFPCAG27 upon PAPD5-siRNA treatment
SAMPLE 10


title: cardiomyocyte,TAC2w, replicate1-62, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: WT-22_biol rep 2


title: K562 cells, 34kpContol, 2


title: SK-N-MC, EGFPCAG27, control-siRNA treatment (rep2)

description:
SK-N-MC cells transfected with EGFPCAG27 upon scramble control siRNA treatment
SAMPLE 9


title: K562 cells, 34kpContol, 1


title: SK-N-MC, Untransfected, PAPD5-siRNA treatment (rep2)

description:
SK-N-MC cells untransfected control upon PAPD5-siRNA treatment
SAMPLE 8


title: WT-22_biol rep 1


title: cardiomyocyte,TAC2w, replicate1-61, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: SK-N-MC, Untransfected, control-siRNA treatment (rep2)

description:
SK-N-MC cells untransfected control upon scramble control siRNA treatment
SAMPLE 7


title: cardiomyocyte,TAC2w, replicate1-60, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: cardiomyocyte,TAC2w, replicate1-59, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: AH-F98_OFC

city: Madrid

first: Alejandro

last: Higuera-Matas

state: Madrid

address: Calle Juan del Rosal 10

department: Psychobiology

country: Spain

institute: Universidad Nacional de Educación a Distancia (UNED)

description:
RawfragmentsOFC.xlslx
F98_uned-jun22_S63_R1_001

data_processing:
The TopHat program included in the G-PRO suite (Biotechvana) was used to map and locate the different sequences against the reference genome (Rattus norvegicus Rn6.0.96), obtaining a percentage of correctly mapped reads ranging from 93 to 95%. Fragments of 19,186 and 21,437 genes were found in PBMC and OFC sequencing, respectively, and a global mean fragment cutoff of less than 240 and 360 was applied as an exclusion criterion. This left a total of 11,855 and 13,942 genes considered expressed in each region.
A differential expression analysis was performed using the CuffDiff program, which analyzes the RNA expression of each gene, normalized by its size and the global RNA expression of each sample, and performs a comparison between groups applying false discovery rate (FDR) correction and obtaining Fold Change (FC) values.
Assembly: Rattus norvegicus Rn6.0.96
Supplementary files format and content: Excel file containing raw counts per gene
Supplementary files format and content: RawfragmentsOFC.xlslx is an Excel file containing raw counts per gene with the following label equivalence: Fsalveh_0 Fsalveh_1 Fsalveh_2 d corresponds to F71_uned-jun22_S54_R1_001.fastq F75_uned-jun22_S45_R1_001.fastq and F80_uned-jun22_S52_R1_001.fastq, respectively.  Msalveh_0 Msalveh_1 Msalveh_2 correspond to M71_uned-jun22_S58_R1_001.fastq M84_uned-jun22_S53_R1_001.fastq M87_uned-jun22_S56_R1_001.fastq, respectively. FLPSTHC_0 FLPSTHC_1 FLPSTHC_2 correspond to F68_uned-jun22_S55_R1_001.fastq F96_uned-jun22_S60_R1_001.fastq F98_uned-jun22_S63_R1_001.fastq respectively. MLPSTHC_0 MLPSTHC_1 MLPSTHC_2 correspond to  M60_uned-jun22_S57_R1_001.fastq M64_uned-jun22_S41_R1_001.fastq M96_uned-jun22_S59_R1_001.fastq respectively. FLPSveh_0 FLPSveh_1 FLPSveh_2 correspond to F70_uned-jun22_S61_R1_001.fastq F103_uned-jun22_S46_R1_001.fastq F104_uned-jun22_S62_R1_001.fastq respectively. MLPSveh_0 MLPSveh_1 MLPSveh_2 correspond to M67_uned-jun22_S50_R1_001.fastq M98_uned-jun22_S48_R1_001.fastq M99_uned-jun22_S49_R1_001.fastq respectively. FsalTHC_0 FsalTHC_1 FsalTHC_2 correspond to F84_uned-jun22_S42_R1_001.fastq F88_uned-jun22_S43_R1_001.fastq F93_uned-jun22_S47_R1_001.fastq respectively. MsalTHC_0 MsalTHC_1 MsalTHC_2 correspond to M76_uned-jun22_S44_R1_001.fastq M83_uned-jun22_S40_R1_001.fastq M92_uned-jun22_S51_R1_001.fastq respectively.

organism: Rattus norvegicus

source_name: Brain (Orbitofrontal cortex)

extract_protocol:
For RNA extraction, the samples were homogenized in homogenization buffer (50mM HEPES, pH 7.5, 320mM sucrose, 20mM sodium butyrate, protein and phosphatase inhibitors in DEPC water). RNA extraction was performed using a column extraction with the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Set (Qiagen) for on-column DNA digestion.
Libraries were prepared using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® UltraTM II Directional RNA Library Prep for Illumina® kits (New England Biolabs), starting from 91 ng of total RNA. The instructions from "Chapter 1: Protocol for use with NEBNext® Poly(A) mRNA Magnetic Isolation Module" were followed. For library amplification as mentioned in the protocol, a 13-cycle PCR was used. For PBMCs, libraries and samples were validated and quantified using the Agilent Bioanalyzer 2100 and Agilent RNA 6000 and Agilent High Sensitivity kits. In the case of the orbitofrontal cortex, both samples and libraries were validated and quantified using the 4200 TapeStation System (Agilent) and RNA Screen Tapes and D1000 Screen Tapes kits.

treatment_protocol: On GD15 and GD16, the rats were injected intraperitoneally, each day, with a dose of 50 µg/Kg of lipopolysaccharides (LPS) 0111:B4 (Sigma-Aldrich) dissolved in sterile saline solution (0.9% NaCl solution; Braun) or with saline, both at a volume of 1 mL/Kg. Increasing doses of THC were administered via intraperitoneal route at a volume of 2 mL/Kg. Between PD30 and PD32, a dose of 2.5 mg/Kg was administered; between PD33 and PD36, the dose was increased to 5 mg/Kg, and finally, between PD37 and PD40, the dose was 10 mg/Kg.

value: Brain (Orbitofrontal cortex)

value: Brain cells

tag: Sex

value: Female

tag: maternal immune_activation

value: LPS

tag: adolescent thc_exposure

value: THC


title: AH-F68_OFC

description:
RawfragmentsOFC.xlslx
F68_uned-jun22_S55_R1_001


title: SK-N-MC, EGFPCAG78, PAPD5-siRNA treatment (rep1)

description:
SK-N-MC cells transfected with EGFPCAG78 upon PAPD5-siRNA treatment
SAMPLE 6


title: AH-F96_OFC

description:
RawfragmentsOFC.xlslx
F96_uned-jun22_S60_R1_001


title: K562 cells, 34kn, 1

value: bone marrow

value: human erythroleukemic cells

tag: genotype


title: SK-N-MC, EGFPCAG78, control-siRNA treatment (rep1)

description:
SK-N-MC cells transfected with EGFPCAG78 upon scramble control siRNA treatment
SAMPLE 5


title: AH-F104_OFC

description:
RawfragmentsOFC.xlslx
F104_uned-jun22_S62_R1_001

value: Vehicle


title: cardiomyocyte,TAC2w, replicate1-58, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

tag: strain

tag: age


title: SK-N-MC, EGFPCAG78, control-siRNA treatment (rep2)

description:
SK-N-MC cells transfected with EGFPCAG78 upon scramble control siRNA treatment
SAMPLE 11


title: WT-28_biol rep 1

value: Seedling

value: 10 days old seedlings


title: K562 cells, 34knContol, 3


title: bacteria in mineral water, day 7, replicate 2

value: suspension in mineral water, after seven day


title: cardiomyocyte,TAC2w, replicate1-57, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte

value: heart


title: K562 cells, 34knContol, 2


title: SK-N-MC, EGFPCAG27, control-siRNA treatment (rep1)

description:
SK-N-MC cells transfected with EGFPCAG27 upon scramble control siRNA treatment
SAMPLE 3

value: Human neuroblastoma cell line SK-N-MC


title: AH-F103_OFC

description:
RawfragmentsOFC.xlslx
F103_uned-jun22_S46_R1_001


title: cardiomyocyte,TAC2w, replicate1-56, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: 6-8 weeks old


title: SK-N-MC, EGFPCAG27, PAPD5-siRNA treatment (rep1)

description:
SK-N-MC cells transfected with EGFPCAG27 upon PAPD5-siRNA treatment
SAMPLE 4


title: K562 cells, 34knContol, 1


title: AH-F70_OFC

description:
RawfragmentsOFC.xlslx
F70_uned-jun22_S61_R1_001


title: K562 cells, 34kn, 3


title: cardiomyocyte,TAC2w, replicate1-55, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: K562 cells, 34kn, 2


title: AH-F93_OFC

description:
RawfragmentsOFC.xlslx
F93_uned-jun22_S47_R1_001

value: Saline

value: THc


title: cardiomyocyte,TAC2w, replicate1-54, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: shNT-5d-Dox-2

city: Houston

first: Yue

last: Lu

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Adapter sequences were removed from the 3' ends of reads using Trim Galore! (version 0.6.5) and cutadapt (version 2.8).
The reads were then aligned to the human genome (hg38) using TopHat (version 2.0.10).
The number of fragments for each known gene from GENCODE Release 37 was quantified using htseq-count from the HTSeq package (version 0.11.0). Genes with fewer than 10 fragments in all samples were removed.
CPM (count per million fragments) values were estimated by the R/Bioconductor package edgeR (version 3.8.6).
Assembly: hg38
Supplementary files format and content: The first column is Ensembl gene id. The second column is gene symbol. The other columns are CPM values (estimated by edgeR) for all the genes in each sample.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen). RNA samples were treated with RNase-free DNase set (Qiagen). 1 μg of total RNA was used for library construction.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit.

treatment_protocol: Cells were treated with 1 µg/ml Doxycycline for 3 or 5 days.

value: multiple myeloma

value: WT

value: Doxycycline

tag: time

value: Day 5


title: AH-F88_OFC

description:
RawfragmentsOFC.xlslx
F88_uned-jun22_S43_R1_001

value: Brain (Orbitofrontal cortex)

value: Brain cells

value: Female

value: THC


title: SK-N-MC, Untransfected, control-siRNA treatment (rep1)

description:
SK-N-MC cells untransfected control upon scramble control siRNA treatment
SAMPLE 1

value: control-siRNA


title: SK-N-MC, Untransfected, PAPD5-siRNA treatment (rep1)

description:
SK-N-MC cells untransfected control upon PAPD5-siRNA treatment
SAMPLE 2


title: shNT-3d-Dox-2

value: Day 3


title: AH-F80_OFC

description:
RawfragmentsOFC.xlslx
F80_uned-jun22_S52_R1_001

value: Vehicle


title: cardiomyocyte,TAC2w, replicate1-52, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte


title: cardiomyocyte,TAC2w, replicate1-51, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: heart


title: T_foetus_rep2

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
ONT reads were basecalled using guppy. For Giardia lamblia we were using one replicate prepared in this study and two datasets from our previous paper (10.1261/rna.078793.121, GSE168675)
Poly(A) tail length was assesed using nanopolish and reads with poly(A) tail shorter than 15 nt (N. gruberi) or 30 nt (others) were discarded.
Alignment was performed using minimap2
Quantification was performed using featureCounts from Rsubread
Annotation of 3’UTRs, cleavage sites, poly(A) signals and auxiliary elements was done with custom scripts.
Assembly: Entamoeba_histolytica.JCVI-ESG2-1.0.dna_rm.toplevel.
Assembly: GiardiaDB-56_GintestinalisAssemblageAWB_Genome
Assembly: GiardiaDB-56_GintestinalisAssemblageBGS_Genome
Assembly: GiardiaDB-56_GmurisRobertsThomson_Genome
Assembly: Naegleria_gruberi_gca_000004985.V1.0.dna_rm.toplevel
Assembly: TrichDB-56_TvaginalisG3_Genome
Assembly: TrichDB-56_TfoetusK_Genome
Supplementary files format and content: Tab separated files with feature counts gene quantifications for every replicate in every organism together with genes coordinates.

organism: Tritrichomonas foetus

source_name: protist cells

growth_protocol: Giardia strains were grown in Keister’s modified TYI-S-33 medium, Trichomonas vaginalis and Tritrichomonas foetus were grown in trypticase-yeast extract maltose (TYM) medium, supplemented with 10% horse serum (Omega), 0.74% ammonium iron (II) sulfate hexahydrate (Sigma-Aldrich) and 1% penicillin-streptomycin (Sigma-Aldrich), and adjusted to pH 6.2. Entamoeba histolitica was grown in TYI-S-33 medium. All were grown axenically at 37ºC under anaerobic conditions. Naegleria gruberi was grown in M7 media in 26ºC.

extract_protocol:
RNA was extracted using TRIZOL reagent.
Nanopore libraries were prepared according to the direct RNA sequencing protocol from ONT (SQK-RNA002). Because the lengths of poly(A) tails were unknown when we initiated this study, total RNA was used in place of oligo(dT)-selected RNA. Libraries were sequenced on a FLO-MIN106 flow cell and minION sequencing device.
Oxford Nanopore Technology direct RNA sequencing

treatment_protocol: Giardia spp, E. histolitica, T. vaginalis and T. foetus were grown in log phase to no more than 80% confluence, detached by cooling on ice (E. histolytica and Giardia) or by vigorous shaking (others), and washed twice by centrifugation and resuspension in ice-cold PBS. The washed pellets were lysed in TRI Reagent (Zymo research) and RNA was extracted and purified using Direct-zol RNA Miniprep Kit (Zymo research) following the manufacturer’s instructions. Total RNA concentration and purity (A260/A280 ratio) were quantified using a NanoDropTM 1000 instrument (Thermo Fisher Scientific). RNA concentrations were >200 ng/µl and A260/A280 ratios >2.0 for all samples. Cell harvesting and RNA extraction were repeated for each parasite strain on three different three different days. Between 2X10^6 and 5X10^6 N. gruberi cells (on their 5th, 6th, or 7th passage after thawing liquid nitrogen stocks) were washed once in 2 mM Tris and spun down at 1500 RCF in a Beckman Coulter microfuge 20R at room temperature. The supernatant was aspirated, and the pellet was suspend in 1 ml TRIzol, vortexed, and promptly stored at -80 C until RNA extractions. The samples were lysed using FastPrep homogenizer with bead beating in TRIzol. Lysate was cleaned up using a Zymo kit with on column DNase treatment. Finally eluted in kit provided MQ water (40 ul). RNA integrity was vrified on Qubit.

value: protist cells


title: T_foetus_rep3


title: AH-F75_OFC

description:
RawfragmentsOFC.xlslx
F75_uned-jun22_S45_R1_001


title: shADA2B-5d-Dox-2

value: ADA2B knockdown


title: T_foetus_rep1


title: cardiomyocyte,TAC2w, replicate1-50, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: 6-8 weeks old


title: AH-F71_OFC

description:
RawfragmentsOFC.xlslx
F71_uned-jun22_S54_R1_001

value: Saline


title: shADA2B-3d-Dox-2

value: multiple myeloma


title: cardiomyocyte,TAC2w, replicate1-49, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: cardiomyocyte,TAC2w, replicate1-48, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: N_gruberi_rep2

organism: Naegleria gruberi


title: shADA2B-5d-Dox-1


title: shNT-5d-Dox-1

value: WT


title: shADA2B-3d-Dox-1

value: Doxycycline


title: N_gruberi_rep1


title: AH-F84_OFC

description:
RawfragmentsOFC.xlslx
F84_uned-jun22_S42_R1_001


title: AH-M96_OFC

description:
RawfragmentsOFC.xlslx
M96_uned-jun22_S59_R1_001

value: Male

value: LPS


title: N_gruberi_rep3


title: AH-M60_OFC

description:
RawfragmentsOFC.xlslx
M60_uned-jun22_S57_R1_001

value: Brain (Orbitofrontal cortex)

value: Brain cells


title: cardiomyocyte,TAC2w, replicate1-53, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: cardiomyocyte,TAC2w, replicate1-46, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: AH-M64_OFC

description:
RawfragmentsOFC.xlslx
M64_uned-jun22_S41_R1_001

value: THC


title: FLAG-3xHA_IgG_TechRep-3

data_processing:
Adapter sequences were removed from the 3' ends of reads using Trim Galore! (version 0.6.5) and cutadapt (version 2.8).
The reads were then mapped to the human genome (hg38) using Bowtie (version 1.1.2) with the following parameters: "--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. Moreover, fragments longer than 800 bp (less than 1% of the total) were excluded from subsequent analysis.
Peaks were identified using MACS2 (version 2.2.7.1) by comparing against the corresponding IgG sample. MACS2 was configured to call peaks from the pile-up of 151 bp around the middle point of each fragment. A q-value cutoff of 0.05 was applied.
The peaks that overlapped with ENCODE blacklisted regions were removed.
Assembly: hg38
Supplementary files format and content: Peak location in bed format
Library strategy: CUT&RUN

extract_protocol:
MM.1S cells expressing either FLAG-3xHA or FLAG-3xHA-ADA2B were subjected to light crosslinking with 0.1% formaldehyde for 1 minute, followed by quenching with 125 mM glycine. Remaining steps of CUT&RUN were performed according to published protocols (Meers et al. 2019) with some modifications. Briefly, 500,000 cells were immobilized to activated Concanavalin A-coated magnetic beads (Bangs Laboratories) followed by permeabilization with wash buffer containing Digitonin (Promega). Samples were incubated with rabbit IgG (Millipore), H3K9ac (Diagenode) and HA (Cell Signaling Technology) antibodies overnight at 4°C. Targeted chromatin digestion was achieved by pAG-MNase (EpiCypher) binding for 10 minutes at room temperature followed by incubation with CaCl2 at 4°C. DNA fragments were purified using MinElute columns (Qiagen).
Libraries were prepared using NEBNext Ultra II DNA Library prep kit (New England Biolabs) following manufacturer’s instructions for H3K9ac CUT&RUN DNA, and a modified library preparation protocol for HA CUT&RUN DNA as described previously (Liu et al. 2018).

tag: cut&run antibody

value: IgG (Millipore)


title: shNT-3d-Dox-1

value: Day 3


title: G_muris_rep2

organism: Giardia muris


title: AH-M99_OFC

description:
RawfragmentsOFC.xlslx
M99_uned-jun22_S49_R1_001

value: Vehicle


title: FLAG-3xHA_IgG_TechRep-2


title: cardiomyocyte,TAC2w, replicate1-47, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte


title: AH-M98_OFC

description:
RawfragmentsOFC.xlslx
M98_uned-jun22_S48_R1_001


title: FLAG-3xHA_IgG_TechRep-1


title: E_histolitica_rep3

organism: Entamoeba histolytica

value: HM1-IMSS (ATCC 30459)


title: G_muris_rep1

value: protist cells


title: cardiomyocyte,TAC2w, replicate1-45, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: heart


title: FLAG-3xHA_H3K9ac_TechRep-3

value: H3K9ac (Diagenode)


title: AH-M67_OFC

description:
RawfragmentsOFC.xlslx
M67_uned-jun22_S50_R1_001


title: cardiomyocyte,TAC2w, replicate1-43, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: 6-8 weeks old


title: AH-M92_OFC

description:
RawfragmentsOFC.xlslx
M92_uned-jun22_S51_R1_001

value: Saline


title: E_histolitica_rep2


title: E_histolitica_rep1


title: FLAG-3xHA_H3K9ac_TechRep-2

value: multiple myeloma


title: AH-M83_OFC

description:
RawfragmentsOFC.xlslx
M83_uned-jun22_S40_R1_001


title: cardiomyocyte,TAC2w, replicate1-42, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: cardiomyocyte,TAC2w, replicate1-41, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: FLAG-3xHA_H3K9ac_TechRep-1


title: AH-M76_OFC

description:
RawfragmentsOFC.xlslx
M76_uned-jun22_S44_R1_001


title: cardiomyocyte,TAC2w, replicate1-40, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: 16Gy_TPOm

city: Bronx

first: Jeb

last: English

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: 10x  Genomics

data_processing:
Demultiplexing, barcode aligning and processing were done usoing Cell Ranger v2.2.1
Assembly: mm10
Supplementary files format and content: Tab separated values and matrix files
Library strategy: scRNAseq/CITEseq/total RNAseq

source_name: Lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resusupended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains and Illumina R1 primer sequence, Unique Molecular Identifier (IMU) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, aplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: For whole thoracic irradiation (WTI) at 16Gy, mice were anesthetized with 60:9 mg/kg ketamine:xylazine, which was equivalent to about 100 μL/mouse, and placed in a lead shielded chamber. The lead shields were placed so that only the thorax was exposed to the radiation field at 1.91 Gy/min. Either TPOm or its vehicle were injected once subcutaneously at the nape, 24 hours before-WTI. Mice were dosed at 1.0 mg/kg. Single cells were isolated using flow cytometry.

value: Lung

value: Wildtype

value: WTI + TPOm treated


title: 16Gy_Vehicle

description: 10x  Genomics

value: WTI + Vehicle treated


title: AH-M87_OFC

description:
RawfragmentsOFC.xlslx
M87_uned-jun22_S56_R1_001

value: Brain (Orbitofrontal cortex)

value: Brain cells

value: Male


title: AH-M84_OFC

description:
RawfragmentsOFC.xlslx
M84_uned-jun22_S53_R1_001


title: cardiomyocyte,TAC2w, replicate1-39, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: FLAG-3xHA-ADA2B_IgG_TechRep-3

value: IgG (Millipore)


title: cardiomyocyte,TAC2w, replicate1-38, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Arid5a iCLIP2 Replicate 3

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

country: Germany

institute: Goethe University Frankfurt

data_processing:
Quality control: FastQC (v0.11.9)
Barcode and adapter trimming: Flexbar (v3.5.0) with non-default parameters: flexbar --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcode.fasta
Mapping: STAR (v2.7.3a) with non-default parameters: STAR --sjdbGTFfile gencode.vM23.primary_assembly.annotation.gtf --sjdbOverhang 76 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate (output: SAMPLE.mapped.bam)
Remove reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): Samtools (v1.10), bedtools (v2.29.2): samtools view -H SAMPLE.mapped.bam > SAMPLE.header; samtools view SAMPLE.mapped.bam > SAMPLE.body; bedtools bamtobed -i SAMPLE.mapped.bam | sort -k1,1 > SAMPLE.mapped.bed; join -t $'\t' -j1 -e "NA" -a1 SAMPLE.mapped.bed CHROMOLENGTHTABLE > SAMPLE.mapped.len.bed; cat SAMPLE.mapped.len.bed | awk '{if(($2==0) || ($3>=$7)) printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6;}' > SAMPLE.idlist; awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.idlist SAMPLE.body > SAMPLE.body.filtered; cat SAMPLE.header SAMPLE.body.filtered | samtools view -b - > SAMPLE.bam
Duplicate removal: UMI-tools (v1.1.2) with non-default parameters: umi_tools dedup -I SAMPLE.bam -S SAMPLE.duprm.bam --method unique –random-seed=100
BAM to BED shifting one base upstream: bedtools (v2.29.2): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.29.2): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v385)
Assembly: GRCm38.p6 (Gencode release M23)
Supplementary files format and content: bigWig files containing the genomic coordinates and duplicate removed counts of uniquely mapped X-links for each replicate separated by strand.

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and penicilin/streptomycin antibiotics at 37˚C with 5% CO2 and 21% oxygen.

extract_protocol:
Cells were lysed and treated with RNase I. Arid5a was immunoprecipitated with Gamma binding beads coupled to anti-GFP antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer and a second adapter containing a barcode was ligated to the cDNAs. The cDNA was pre-amplified for 6 cycles using short Solexa P3 and P7 primers. After a size selection on beads a second PCR amplification was performed with the normal P3 and P7 primers to generate the final iCLIP2 libraries.
iCLIP2

treatment_protocol: Cells were transfected with a plasmid containing murine Arid5a-GFP. After 24 h cell were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

value: transfected with Arid5a-GFP

value: WT

value: anti-GFP antibody

tag: barcode sequence

value: NNNNNCACTGTNNNN

tag: fraction

value: Arid5a-bound RNA


title: cardiomyocyte,TAC2w, replicate1-44, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte

value: heart


title: FLAG-3xHA-ADA2B_IgG_TechRep-2


title: FLAG-3xHA-ADA2B_HA_TechRep-3

value: HA (CST)


title: Arid5a iCLIP2 Replicate 2

value: NNNNNGCCTAANNNN


title: Non_irradiated

description: 10x  Genomics

value: Lung

value: No WTI


title: AH-F96_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F96_S23_L002_R1_001

source_name: Blood

value: Blood

value: peripheral blood mononucelar cells

value: Female

value: LPS

value: THC


title: FLAG-3xHA-ADA2B_HA_TechRep-2

value: multiple myeloma


title: shNT-5d-Dox-2

data_processing:
Adapter sequences were removed from the 3' ends of reads using Trim Galore! (version 0.6.5) and cutadapt (version 2.8).
The reads were then mapped to the human genome (hg38) using Bowtie (version 1.1.2) (Langmead et al. 2009) with the following parameters: "--allow-contain --maxins 2000 -v 2 -m 1 --best --strata". To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis.
After the removal of fragments from chrM, for each fragment, the 5’ end was offset by +4 bp and the 3’ end was offset by -5 bp to adjust both ends to represent the center of a transposon binding event.
For each sample, peaks were identified using MACS2 (version 2.2.7.1) without using any control. Each binding event (i.e., the 5’ or 3’ end of a fragment) was smoothed by 73 bp (i.e., extended 36 bp upstream and 36 bp downstream from the event center). MACS2 was configured to call peaks from the pile-up of smoothed binding events, and a q-value cutoff of 0.001 was applied.
The peaks that overlapped with ENCODE blacklisted regions (Amemiya et al. 2019) were removed.
Assembly: hg38
Supplementary files format and content: Peak location in bed format

extract_protocol:
The Tn5 transposition reaction was performed using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina). For each sample 100,000 cells were collected and washed with cold PBS. A resuspension buffer (10 nM Tris-HCl, pH7.5, 10 mM NaCl, 3 mM MgCl2) was used for subsequent steps. Cells were lysed in 100 μl lysis buffer (0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin in resuspension buffer) on ice for 3 minutes, then washed with 1 ml wash buffer (0.1% Tween-20 in resuspension buffer). Lysates were cleared by centrifugation at 500g, 4°C for 10 minutes. The nuclear pellet was resuspended in 100 μl transposition reaction mix (50 μl Tagment DNA Buffer, 33 μl PBS, 1 μl 10% Tween-20, 1 μl 1% Digitonin, 5 μl TDE1, 10 μl nuclease-free water) and incubated at 37°C on a thermomixer with 1,000 rpm for 30 minutes. DNA was isolated using the Qiagen MinElute Reaction Cleanup Kit (Qiagen).
Library was prepared with NEBNext High-Fidelity 2X PCR Master Mix (NEB) and SYBR Green I (ThermoFisher).

value: Doxycycline

value: Day 5


title: AH-M71_OFC

description:
RawfragmentsOFC.xlslx
M71_uned-jun22_S58_R1_001

value: Brain (Orbitofrontal cortex)

value: Brain cells

value: Male

value: Saline

value: Vehicle


title: cardiomyocyte,TAC2w, replicate1-37, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: Arid5a iCLIP2 Replicate 1

value: transfected with Arid5a-GFP

value: WT

value: anti-GFP antibody

value: NNNNNACATCGNNNN

value: Arid5a-bound RNA


title: cardiomyocyte,TAC2w, replicate1-36, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: shNT-5d-Dox-1


title: cardiomyocyte,TAC2w, replicate1-35, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: AH-F67_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F67_S14_L002_R1_001

value: Blood

value: peripheral blood mononucelar cells

value: Female

value: LPS

value: THC


title: DC+Allo specificTem3

city: Cincinnati

first: Irene

last: Saha

state: Ohio

address: 3333 Burnet Avenue

department: Immunobiology

institute: Cincinnati Children's Hospital and Medical center

description:
NextSeq SE-50 High Output V2 flow cell
AlloTem3

data_processing:
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed on CLC Genomics Workbench 7 (Qiagen).
The expression of the genes in all samples was calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Assembly: mm10
Supplementary files format and content: .txt, raw_counts matrix that contains all gene names and counts for each sample

source_name: CD11b+ CD11c+ splenic DCs cultured with Allo specific Tem, replicate-3

growth_protocol: B6 mice were injected with B16  cells secreting Flt3 ligand. Spleens were extracted from mice once the tumor was 1 cm in diameter. Splenic DCs were isolated by negatively selecting out T, B,NK cells and macrophages using Mojosort beads.

extract_protocol:
RNA prep for mRNA-sequencing was performed using the miRNeasy (Qiagen) and treated with DNase I (Qiagen), according to the manufacturer's instructions. Quantities of extracted RNA were determined using NanoDrop2000 for cDNA synthesis or Agilent Bioanalyzer 2100 before RNA-Seq Library preparation.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100.

treatment_protocol: B6 DCs were cultured alone or with LPS or in the presence of B6 syngeneic or BALB/c derived alloantigen-specific memory T cells for 3 hours.Splenic DCs were sorted from cultures on the basis of CD11b and CD11c expression using Sony MA900 sorter.

value: Spleen

value: Dendritic cells

value: DC+Allo specific Tem


title: DC+Allo specific Tem2

description:
NextSeq SE-50 High Output V2 flow cell
AlloTem2

source_name: CD11b+ CD11c+ splenic DCs cultured with Allo specific Tem, replicate-2


title: shNT-3d-Dox-2

value: multiple myeloma

value: Doxycycline

value: Day 3


title: cardiomyocyte,TAC2w, replicate1-34, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: shNT-3d-Dox-1

value: WT


title: AH-F103_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F103_S24_L002_R1_001

value: Vehicle


title: AH-F104_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F104_S25_L002_R1_001


title: cardiomyocyte,TAC2w, replicate1-33, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: shADA2B-5d-Dox-1

value: ADA2B knockdown

value: Day 5


title: cardiomyocyte,TAC2w, replicate1-32, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: DC+Syngeneic Tem3

description:
NextSeq SE-50 High Output V2 flow cell
SynTem3

source_name: CD11b+ CD11c+ splenic DCs cultured with Syngeneic Tem, replicate-3

value: DC+Syngeneic Tem


title: DC+Syngeneic Tem2

description:
NextSeq SE-50 High Output V2 flow cell
SynTem2

source_name: CD11b+ CD11c+ splenic DCs cultured with Syngeneic Tem, replicate-2


title: cardiomyocyte,TAC2w, replicate1-31, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

source_name: heart


title: shADA2B-5d-Dox-2


title: DC+ Syngeneic Tem1

description:
NextSeq SE-50 High Output V2 flow cell
SynTem1

source_name: CD11b+ CD11c+ splenic DCs cultured with Syngeneic Tem, replicate-1


title: DC+Allo specific Tem1

description:
NextSeq SE-50 High Output V2 flow cell
AlloTem1

source_name: CD11b+ CD11c+ splenic DCs cultured with Allo specific Tem, replicate-1


title: shADA2B-3d-Dox-2


title: AH-F68_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F68_S15_L002_R1_001

value: Blood

value: peripheral blood mononucelar cells

value: Female


title: AH-F83_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F83_S20_L002_R1_001

value: Saline

value: THC


title: DC+LPS3

description:
NextSeq SE-50 High Output V2 flow cell
LPS3

source_name: CD11b+ CD11c+ splenic DCs, LPS stimulated, replicate-3

value: Spleen

value: Dendritic cells

value: DC+LPS


title: cardiomyocyte,TAC2w, replicate1-29, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: cardiomyocyte,TAC2w, replicate1-30, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: shADA2B-3d-Dox-1

value: multiple myeloma

value: Doxycycline

value: Day 3


title: AH-F78_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F78_S18_L002_R1_001


title: DC+LPS2

description:
NextSeq SE-50 High Output V2 flow cell
LPS2

source_name: CD11b+ CD11c+ splenic DCs, LPS stimulated, replicate-2


title: AH-F91_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F91_S21_L002_R1_001


title: DC+LPS1

description:
NextSeq SE-50 High Output V2 flow cell
LPS1

source_name: CD11b+ CD11c+ splenic DCs, LPS stimulated, replicate-1


title: cardiomyocyte,TAC2w, replicate1-28, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: cardiomyocyte,TAC2w, replicate1-27, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: AH-F80_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F80_S19_L002_R1_001

value: Vehicle


title: AH-F69_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F69_S16_L002_R1_001

value: LPS


title: SW872 Eribulin

city: Beijing

first: Jianhui

last: Wu

address: No.52 Fucheng Road, Haidian District

department: Department of Hepato-Pancreato-Biliary Surgery

institute: Peking University Cancer Hospital & Institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: Homo sapiens.GRCh38
Supplementary files format and content: reads value formated in csv file

molecule: polyA RNA

growth_protocol: 94T778 and Sw872 cell lines were acquired from American Type Culture Collection, and routinely cultured in RPMI 1640 medium supplemented with 10% FBS

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

treatment_protocol: 93T449, 94T778 and Sw872 cells were treated with anlotinib and eribulin for 24 hours, at which concentration reached maximum synergy score.

value: liposarcoma

value: wild type

value: eribulin 24h treatment


title: SW872 Anlotinib

value: anlotinib 24h treatment


title: DC only 3

description:
NextSeq SE-50 High Output V2 flow cell
DC3

source_name: CD11b+ CD11c+ splenic DCs, unstimulated, replicate-3

value: DC only


title: cardiomyocyte,TAC2w, replicate1-26, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: AH-F94_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F94_S22_L002_R1_001

value: Blood

value: peripheral blood mononucelar cells

value: Female

value: Saline

value: THc


title: DC only 2

description:
NextSeq SE-50 High Output V2 flow cell
DC2

source_name: CD11b+ CD11c+ splenic DCs, unstimulated, replicate-2

value: Spleen

value: Dendritic cells


title: AH-F71_PBMC

description:
RawfragmentsPBMC.xlsx
AH-F71_S17_L002_R1_001


title: AH-M64_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M64_S27_L002_R1_001

value: Male

value: THC


title: SW872 Control

value: control


title: cardiomyocyte,TAC2w, replicate1-24, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte

value: heart

value: 6-8 weeks old


title: cardiomyocyte,TAC2w, replicate1-25, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: 94T778 Combination

value: liposarcoma

value: wild type

value: combination 24h treatment


title: AH-M63_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M63_S26_L002_R1_001

value: LPS


title: 94T778 Eribulin

value: eribulin 24h treatment


title: Cyp27a1_E18_KO-KO (3_KO)

city: Lund

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

country: Sweden

institute: Lund university

description: Sample 4

data_processing:
data procesing and analysis using Cell ranger, version 3.0.0)
Seurat_4.3.0
followed seurat Vignette for clustering: normalization, find variable genes, data scaling and linear and non linear dimensionality reduction
nFeature_RNA > 200 & nFeature_RNA < 7500 & percent.mt < 5)
KenichiAll(Seurat object) was then subsetted for the objects E1 and E2 based on the data from embryonic day 14.5 and 18.5
Assembly: mm10
Supplementary files format and content: Cell ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
Supplementary files format and content: Annotation_table.txt

source_name: E18.5 Lung cells of Cyp27a1-/- fetuses grown in Cyp27a1-/- mother

extract_protocol:
Lungs extracted from E14.5 and E18.5 embryos were minced and digested using collagenase I and dispase I (both 1 mg/mL, Roche) and incubated at 37°C for 5 min. for twice. The cells were transferred to a 50 ml tube through a 100 μm cell strainer. After rinsing the cell strainer with 1 ml of PBS twice, 5 ml of PBS was added to the tube through the cell strainer. The cell suspension was transferred to a new 50 ml tube through a 40 μm cell strainer. Cells were collected by centrifugation at 200 x g for 5 min. and re-suspended with 1 ml of NH4Cl for red blood cell lysis. After adding 5 ml of the staining medium, the cells were then transferred to a 15 ml tube through 50 μm filter and centrifuged for 5 min at 200 x g.
cDNA Library constructed using Chromium system (10x Genomics)

value: Lung

value: fetal Lung cells

tag: group

value: grown in Cyp27a1-/- mother


title: AH-M60_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M60_S28_L002_R1_001

value: Blood

value: peripheral blood mononucelar cells


title: Cyp27a1_E18_HT-KO (4_WT)

description: Sample 3

source_name: E18.5 Lung cells of Cyp27a1-/- fetuses grown in Cyp27a1+/- mother

value: grown in Cyp27a1+/- mother


title: AH-M100_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M100_S37_L002_R1_001

value: Male

value: Vehicle


title: 94T778 Control

value: control


title: SW872 Combination


title: Cyp27a1_E14_KO-KO (2_KO_KO)

description: Sample 2

source_name: E14.5 Lung cells of Cyp27a1-/- fetuses grown in Cyp27a1-/- mother


title: AH-M98_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M98_S36_L002_R1_001


title: cardiomyocyte,TAC2w, replicate1-21, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte


title: Cyp27a1_E14_HT-KO (1_HT_KO)

description: Sample 1

source_name: E14.5 Lung cells of Cyp27a1-/- fetuses grown in Cyp27a1+/- mother


title: AH-M68_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M68_S29_L002_R1_001

source_name: Blood


title: DC only 1

description:
NextSeq SE-50 High Output V2 flow cell
DC1

source_name: CD11b+ CD11c+ splenic DCs, unstimulated, replicate-1

value: Spleen

value: Dendritic cells

value: DC only


title: Hs3st3a1;3b1 DKO male_SMG-3000

city: Bethesda

first: Vaishali

middle: N

last: Patel

state: Maryland

address: 9000 Rockville Pike

department: NIDCR

institute: National Institutes of Health

data_processing:
Basecalls performed using Illumina’s RTA 2.0.12
Sequenced reads were mapped to GRCh38.v25human genome using STAR v2.5.2a in single-pass mode with the following parameters: --outFilterMultimapNmax 20 –outFilterType BySJout --alignSJoverhangMin 1 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: mm10
Supplementary files format and content: Raw counts expression matrix.
Supplementary files format and content: Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: TMM-normalized Counts Per Million expression matrix.

source_name: Submandibular Gland

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on a HiSeq2500 sequencer (Illumina).

value: Submandibular Gland

value: double knockout

value: male


title: cardiomyocyte,TAC2w, replicate1-20, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: heart

value: 6-8 weeks old


title: 93T449 Eribulin

value: liposarcoma

value: wild type

value: eribulin 24h treatment


title: cardiomyocyte,TAC2w, replicate1-23, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: 94T778 Anlotinib

value: anlotinib 24h treatment


title: 93T449 Control


title: cardiomyocyte,TAC2w, replicate1-22, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: AH-M76_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M76_S30_L002_R1_001

value: Blood

value: peripheral blood mononucelar cells

value: Saline

value: THC


title: 93T449 Anlotinib


title: cardiomyocyte,TAC2w, replicate1-18, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte


title: AH-M91_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M91_S34_L002_R1_001

value: Male


title: Hs3st3a1;3b1 DKO male_SMG-2764


title: AH-M93_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M93_S35_L002_R1_001


title: AH-M85_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M85_S33_L002_R1_001

value: Vehicle


title: Hs3st3a1;3b1 DKO male_SMG-3701


title: Spheroids D11 13

first: Mark

last: Rochman

state: OH

address: 3333 Burnett Ave

department: Allergy and Immunology

institute: CCHMC

data_processing:
Data was analyzed by CLC genomic benchwork V23.0.5
Sequences were trimmed for the adaptor/low-quality reads using default parameters and aligned to HG38 human genome
Normalization and read count extractions were performed by CLC genomics workbench
Assembly: HG38
Supplementary files format and content: tab-delimited file includes TPM for all samples

source_name: EPC2 cells

growth_protocol: The esophageal hTERT-immortalized human epithelial cell line EPC2 was a gift from Anil Rustgi (Columbia University, New York, New York, USA). Esophageal epithelial spheroids were generated essentially as described in doi:10.1002/cpsc.106. and 10.1136/gutjnl-2022-327166 with minor modifications. Briefly, EPC2 cells were passed through 0.7 um cells strainer and counted. At D0 of the culture, 40,000 cells in a 20 ul droplet of undiluted Matrigel (354234, Corning) were placed in each well of a pre-warmed 12-well plate using a cold wide bore tip. The plate was kept at 37C for 30 min before adding 1 ml of the keratinocyte serum-free medium (17005042, ThermoFisher) with 0.6 mM CaCl2 (KSFMC) containing 10 uM Y27632 (InSolution™ in DMSO, Calbiochem). The medium was replenished with KSFMC without Y27632 every other day starting from D3 of the culture. At the indicated time, the Matrigel drop with spheroids was washed out of the plate in 750 ul of cold PBS/1% BSA without into the Eppendorf tubes with a wide bore tip and processed. Special care was taken not to collect adherent cells that were attached to the plastic.

extract_protocol:
Spheroids were spun down at 500g at 4C for 5 min and the PBS/1% BSA solution was carefully removed. For downstream analyses, the spheroids were recovered from Matrigel in 1 ml of cell recovery solution (354253, Corning) for 30 min on ice with occasional mixing. Spheroids were washed once with 1 ml of cold PBS and lysed in TriPure Isolation Reagent at 700 L/sample (11667165001, Sigma). Chloroform was added at a volume of 140 uL per sample, and the tubes were shaken vigorously for 15 seconds and allowed to stand at room temperature for 10-15 minutes. Samples were centrifuged at 12,000 g for 15 minutes at 48C, after which 350 mL of the upper aqueous phase was collected and mixed at a 1:1 ratio with 100% ethanol. Further isolation was performed by using the Quick-RNA MicroPrep Kit (Zymo Research, Irvine, Calif, catalog no. R1051) per the manufacturer’s instructions. The RNA concentration was measured by Nanodrop, and the RNA integrity number was determined by the Gene Expression Core at CCHMC by using the Agilent 2100 Bioanalyzer.
Standard Illumina protocol

treatment_protocol: For bulk RNA sequencing, the spheroids were differentiated for 11 days, and RNA was collected at D0 before the cells were seeded, at D3 and D11 of the culture. For differentiation in the presence of IL-13, spheroids were treated with IL-13 (Peprotech, Rocky Hill, NJ, catalog no. 200-13) at 20 ng/ml from D3 till D11. Medium was replenished every other day.

tag: batch

value: EPC2 cells

value: esophageal epithelial

value: WT


title: Spheroids D3 9

value: UT


title: cardiomyocyte,TAC2w, replicate1-15, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

tag: tissue

value: heart


title: 93T449 Combination

tag: cell type

value: combination 24h treatment


title: AH-M79_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M79_S32_L002_R1_001


title: WT_male SMG-3729

value: Submandibular Gland

value: Wildtype

value: male


title: cardiomyocyte,TAC2w, replicate1-19, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: 6-8 weeks old


title: cardiomyocyte,TAC2w, replicate1-14, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Monolayer 10


title: WT_male SMG-2948


title: cardiomyocyte,TAC2w, replicate1-17, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Hs3st3a1;3b1 DKO male_SMG-2994

value: double knockout


title: Spheroids D11 7


title: Sham snRNA-seq rep2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
The reads were aligned to rat reference genome (rn7; ENSEMBL, version 67) using CellRanger v6.1.1 with default parameters, excluding the option ‘-include-introns’ to obtain intronic reads in nuclei.
Assembly: mRatBN7 (rn7)
Supplementary files format and content: Tab-separated files and matrix files

molecule: nuclear RNA

source_name: infarct zone

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615; Promega and AM2696; Life Technologies). Heart samples were cut into 2-mm pieces and homogenized using a Dounce homogenizer (885302-0002; Kimble Chase)  in 2 ml of ice-cold Nuclei EZ Lysis buffer, and they were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-mm cell strainer (43-50040-51; pluriSelect) and then centrifuged at 5003g for 5 minutes at 4°C. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (1xPBS, 0.07% BSA, and 0.1% RNase inhibitor), filtered through a 20-mm cell strainer (43-50020-50; pluriSelect), and counted.
cDNA libraries were constructed using Chrominum Single-Cell 3’GEM, Library & Gel Bead Kit v3, then sequenced on illumina novaseq 6000.

value: infarct zone

value: Sham


title: cardiomyocyte,TAC2w, replicate1-16, scRNAseq

institute: The University of Tokyo

description:
smartseq2
TAC2w_1.xlsx

source_name: heart


title: WT_male SMG-2761


title: Monolayer 9


title: Sham snRNA-seq rep1


title: 4T1 NEG rep 3

city: Buffalo

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
4T1-AxR-SM-NEG-3
RS-03036554

data_processing:
Pre-alignment quality control was performed using FASTQC v0.11.5.
Sequenced reads (fastq files) were alinged to the mouse genome GRCm38 M16 (Gencode) using STAR v2.6.0a.
Post-alignment quality control was performed using RSeQC v2.6.5.
Estimated counts at the gene level were quantified using RSEM v1.3.1.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include RSEM estimated counts at the gene level for all samples

growth_protocol: mouse breast tumor cells (4T1) resistant to axitinib were maintained in RPMI1640 supplemented with 5% FBS and 0.5µM Axitinib. Media was replenished every 3 to 4 days.

extract_protocol:
Total RNA from individual samples was extracted using the RNeasy mini kit (QIAGEN; 74104). Genomic DNA was digested using DNase I (QIAGEN; 79254) as described in the on-column DNase digestion protocol from QIAGEN.
One microgram total RNA was used for library preparation using the TruSeq Stranded mRNA kit (Illumina Inc) following manufacturer's instructions.

value: Breast cancer cells

tag: variant

value: 4T1 AXR SM NEG

value: Axitinib

tag: concentration


title: Spheroids D11 12

tag: cell line

tag: treatment


title: cardiomyocyte,TAC2w, replicate1-11, scRNAseq

city: Bunkyo-ku

last: Katoh

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte


title: cardiomyocyte,TAC2w, replicate1-10, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: cardiomyocyte,TAC2w, replicate1-12, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Hs3st3a1;3b1 DKO male_SMG-2749

tag: Sex


title: MI-stiff snRNA-seq rep1

value: MI + stiff hydrogel


title: WT_male SMG-2758


title: 4T1 POS rep 3

description:
4T1-AxR-SM-POS-3
RS-03036553

value: 4T1 AxR SM POS


title: cardiomyocyte,TAC2w, replicate1-13, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Spheroids D11 6

value: EPC2 cells

value: esophageal epithelial

value: WT


title: cardiomyocyte,TAC2w, replicate1-9, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: heart


title: Spheroids D3 8

value: UT


title: MI-soft snRNA-seq rep2

value: MI + soft hydrogel


title: Spheroids D11 5


title: 4T1 NEG rep 2

description:
4T1-AxR-SM-NEG-2
RS-03036552


title: AH-M77_PBMC

description:
RawfragmentsPBMC.xlsx
AH-M77_S31_L002_R1_001

value: Blood

value: peripheral blood mononucelar cells

value: Male

tag: maternal immune_activation

value: Saline

tag: adolescent thc_exposure

value: Vehicle


title: cardiomyocyte,TAC2w, replicate1-8, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

tag: strain

value: 6-8 weeks old


title: MI-soft snRNA-seq rep1

value: infarct zone


title: cardiomyocyte,TAC2w, replicate1-7, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

tag: age


title: Spheroids D11 4

tag: genotype


title: MI snRNA-seq rep2

value: MI


title: MI-stiff snRNA-seq rep2


title: MI snRNA-seq rep1


title: Monolayer 8


title: 4T1 NEG rep 1

description:
4T1-AxR-SM-NEG-1
RS-03036550

value: Breast cancer cells

value: 4T1 AXR SM NEG

value: Axitinib


title: cardiomyocyte,TAC2w, replicate1-6, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: cardiomyocyte


title: Monolayer 7

value: EPC2 cells

value: esophageal epithelial


title: Sham-4

data_processing:
Paired-end 150 bp reads of bulk RNA-seq data were aligned to rn7 reference genome (ENSEMBL, version 67) using STAR alignment tool (version 2.7.3a) with default parameters.
Uniquely mapped reads were employed to quantify gene expression using RSEM software (version 1.3.1).2 Transcripts per million mapped reads (TPM) were calculated to estimate the gene expression levels, normalized for sequencing depth.
Assembly: mRatBN7 (rn7)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM counts for each Sample

extract_protocol:
total RNA was purified from the infarct zone of Sham, MI and MI/R using RNeasy RNA isolation Kit (Qiagen) coupled with an on-column DNase I digestion to eliminate residual DNA. The mRNA was purified from 2 μg of total RNA.
libraries for massive parallel sequencing were constructed with NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB). Library quality was assessed with Agilent Bioanalyzer 2100 system. Next-generation sequencing was performed on an Illumina HiSeq 4000 platform.

value: Sham


title: cardiomyocyte,TAC2w, replicate1-5, scRNAseq

description:
smartseq2
TAC2w_1.xlsx

value: heart


title: Monolayer 6

value: WT

value: UT


title: cardiomyocyte,TAC2w, replicate1-4, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Spheroids D11 3


title: 4T1 POS rep 1

description:
4T1-AxR-SM-POS-1
RS-03036549

value: 4T1 AxR SM POS


title: Sham-2


title: Sham-3


title: Keratinocytes, NFYB, IP

city: Milano

first: Diletta

last: Dolfini

state: MI

address: Via Celoria, 26

department: Bioscience

country: Italy

institute: University of Milan

description: ChIP-seq reads were trimmed to get a final length of 35 bp

data_processing:
ChIP-seq reads were processed using the ENCODE pipeline 2.1.5, setting default peak caller and bowtie2 aligner.
Homo sapiens ChIP-seq reads were aligned to the hg38 v4 genome provided by ENCODE pipeline.
Mus musculus ChIP-seq reads were aligned to the mm10 v4 genome provided by ENCODE pipeline.
Supplementary files format and content: hg38, mm10
Supplementary files format and content: bigWig, bed narrowPeak (except for Input sample)

source_name: Keratinocytes

extract_protocol:
HeLa: material was processed for ChIP.
DNA libraries were prepared using the NEbNext ChIP-Seq Library kit and TruSeq sample prep (Illumina)

treatment_protocol: HeLa cells at 25-30% confluence were transfected with 50 nM siRNA using Lipofectamine 3000 Reagent (ThermoFisher).

value: Keratinocytes

value: Normal

tag: chip antibody

value: NFYB, IP


title: cardiomyocyte,TAC2w, replicate1-3, scRNAseq

first: Manami

address: 7-3-1 Hongo

description:
smartseq2
TAC2w_1.xlsx

value: 6-8 weeks old


title: Keratinocytes, input


title: cardiomyocyte,TAC2w, replicate1-2, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Spheroids D3 7


title: cardiomyocyte,TAC2w, replicate1-1, scRNAseq

description:
smartseq2
TAC2w_1.xlsx


title: Sham-1

value: infarct zone


title: Fetal Myocytes, input

source_name: Fetal Myocytes

value: Fetal Myocytes


title: Fetal Myocytes, NFYB, IP


title: 4T1 POS rep 2

description:
4T1-AxR-SM-POS-2
RS-03036551

value: Breast cancer cells


title: Monolayer 5


title: MI_stiff-4


title: Spheroids D11 2


title: Fetal Myoblasts, NFYB, IP

source_name: Fetal Myoblasts

value: Fetal Myoblasts


title: cardiomyocyte,sham, replicate2-80, scRNAseq

description:
smartseq2
sham_2.xlsx

value: sham


title: MI_stiff-3


title: Fetal Myoblasts, input


title: MI_stiff-2


title: Monolayer 4


title: cardiomyocyte,sham, replicate2-79, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: Spheroids D3 6

value: EPC2 cells


title: cardiomyocyte,sham, replicate2-78, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Monolayer 3

value: esophageal epithelial


title: MI_stiff-1


title: MI_soft-4


title: MoAM VimKO D6 rep2

city: Chicago

first: kishore

last: Anekalla

state: IL

address: 303 E. Superior

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
Fpkm
Genome_build: mm10
Supplementary_files_format_and_content: Fpkm_counts_MoAMs_013019.xlsx

source_name: Lung

extract_protocol: Total RNA was isolated using RNeasy Plus Mini kits (Qiagen). Using poly(A) mRNA magnetic enrichment  kits from NEBNext (New England Biolabs), mRNA was isolated. cDNA libraries were prepared  using NEBNext Ultra DNA library kits (New England BioLabs) for Illumina. Libraries were  sequenced using high-output 75-cycle single-end kits on an Illumina NextSeq 500 sequencer

treatment_protocol: Mice were anesthetized using isoflurane and intratracheally (i.t.) infected with 200 pfu WSN

value: Monocyte derived alveolar macrophages

tag: agent

value: Influenza A virus

tag: time point

value: MoAM VimKO


title: cardiomyocyte,sham, replicate2-76, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: Spheroids D11 1

value: WT

value: UT


title: cardiomyocyte,sham, replicate2-77, scRNAseq

description:
smartseq2
sham_2.xlsx


title: MI_soft-3


title: MoAM VimKO D6 rep1


title: Spheroids D11 11


title: cardiomyocyte,sham, replicate2-75, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Spheroids D3 5


title: MoAM VimKO D4 rep3


title: Monolayer 2


title: MI_soft-2


title: MoAM VimKO D4 rep2


title: cardiomyocyte,sham, replicate2-73, scRNAseq

description:
smartseq2
sham_2.xlsx


title: MI_soft-1


title: cardiomyocyte,sham, replicate2-74, scRNAseq

description:
smartseq2
sham_2.xlsx


title: MI-4

value: MI


title: MoAM VimKO D4 rep1


title: Spheroids D3 4


title: MoAM VimKO D6 rep4


title: cardiomyocyte,sham, replicate2-72, scRNAseq

description:
smartseq2
sham_2.xlsx


title: cardiomyocyte,sham, replicate2-71, scRNAseq

description:
smartseq2
sham_2.xlsx


title: MoAM VimKO D3 rep4


title: MoAM VimKO D6 rep3


title: Spheroids D11 10


title: MI-2


title: Spheroids D3 3


title: cardiomyocyte,sham, replicate2-69, scRNAseq

description:
smartseq2
sham_2.xlsx


title: cardiomyocyte,sham, replicate2-70, scRNAseq

description:
smartseq2
sham_2.xlsx


title: MoAM VimKO D3 rep3


title: MI-1


title: Monolayer 1


title: Spheroids D3 2


title: MI_24H snRNA-seq

data_processing:
The reads were aligned to rat reference genome (rn7; ENSEMBL, version 67) using CellRanger v6.1.1 with default parameters, excluding the option ‘-include-introns’ to obtain intronic reads in nuclei.
The processed data include matrix, gene and barcode, which were produced by CellRanger (v6.1.1) software. Processed data can be loaded by "Read10X" function of Seurat R package. Barcode number "-1", "-2", "-3" and "-4" represents Sham, MI_24h, MI_1h_R and MI_6h_R respectively.
Assembly: rn7
Supplementary files format and content: Tab-separated files and matrix files

value: MI 24h reperfusion

value: Sprague Dawley


title: MoAM VimKO D3 rep2


title: MI_6H snRNA-seq

value: infarct zone

value: MI 6h reperfusion


title: MoAM VimKO D2 rep3


title: Spheroids D11 9


title: cardiomyocyte,sham, replicate2-68, scRNAseq

description:
smartseq2
sham_2.xlsx

value: 6-8 weeks old


title: MoAM VimKO D3 rep1


title: MI_1H snRNA-seq

value: MI 1h reperfusion


title: cardiomyocyte,sham, replicate2-67, scRNAseq

description:
smartseq2
sham_2.xlsx

value: sham


title: Sham snRNA-seq

value: Sham


title: cardiomyocyte,sham, replicate2-66, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: Spheroids D11 8

value: EPC2 cells

value: esophageal epithelial


title: MoAM VimKO D2 rep2

value: Monocyte derived alveolar macrophages

value: Influenza A virus


title: cardiomyocyte,sham, replicate2-65, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: MoAM VimKO D2 rep1

value: MoAM VimKO


title: Spheroids D3 1

value: WT

value: UT


title: Rat_embryos_THAP1_E11.5

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

institute: University of Tuebingen

data_processing:
Read quality of scRNA-seq data in fastq files was assessed using QoRTs (v1.2.37).
The sequencing data were processed using the CellRanger software (v3.0.1) with default parameters and the rn6 rat reference genome.
The expression matrix was extracted from the “filtered_feature_bc_matrix” folder outputted by the CellRanger count pipeline.
The R package Seurat (Version 4.3.0) was used to analyse the digital expression matrix.
Assembly: rn6
Supplementary files format and content: cloupe files

source_name: Embryo

extract_protocol:
Allantois, yolk sac, and embryo were dissected and placed into separate tubes. The whole single embryo was carefully dissected. Single-cell suspensions were prepared by incubating the embryos with Papain solution (2mg/ ml) at 37 degree for 20 min and quenching with DMEM medium supplemented with 5% FBS. After centrifugation, single cell were re-suspended in PBS with 0.1% BSA for single-cell RNA-seq.
Single-cell RNA-seq libraries preparation was performed according to the 10x chromium SC-RNA-seq protocol. After measuring the cell viability, cells were loaded on 10x Chromium Chip. Single cells were prepared in the Chromium Single Cell Gene Expression Solution using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10 × Genomics, CG000204) according to the instruction of manufacturer.

value: Embryo

tag: developmental stage

value: THAP1 KO


title: MoAM WT D6 rep4

value: MoAM WT


title: Control, replicate 3, scRNAseq

city: Hefei

first: Yong

last: Jin

address: No.96, JinZhai Road Baohe District, Hefei, Anhui, 230026, P.R.China.

institute: University of Science and Technology of China

data_processing:
The processed data were made using the Cell Ranger software-4.0.0.
Assembly: GRCh38
Supplementary files format and content: Comma-Separated Values files

source_name: liver

extract_protocol:
Liver tissues were subjected to collagenase digestion and density gradient centrifugation to collect mesenchymal cells.
The 3’Gene Expression Library was constructed with the quality-qualified cDNA.  After fragmentation, adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.

value: liver

tag: subject status

value: liver hemangioma patient

value: hepatic mesenchymal cells


title: cardiomyocyte,sham, replicate2-64, scRNAseq

description:
smartseq2
sham_2.xlsx

tag: tissue

value: 6-8 weeks old

value: sham


title: MoAM WT D6 rep3

tag: cell type


title: Rat_embryos_WT_E10.5

value: Wild-type


title: Control, replicate 2, scRNAseq


title: MoAM WT D6 rep2


title: Control, replicate 1, scRNAseq


title: cardiomyocyte,sham, replicate2-63, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: MoAM WT D6 rep1


title: ExhaustedCART_ATAC-seq Biorep3

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

data_processing:
Quality check was performed first with FASTQC. Then, the Nextera adapter sequences were trimmed and a minimum length of 45 base-pairs was employed per ENCODE recommendations using Cutadapt. FASTQC was then re-run to ensure quality. Next, paired-end reads for each sample were aligned to the UCSC reference genome for human genome 38 (hg38), patch release 13 with Bowtie2. The resulting bam file was sorted with samtools and mitochondrial reads were removed with the BAMQC program. BigWig files were created from sorted BAM files using the bamCoverage function.
Assembly: UCSC reference genome for human genome 38 (hg38), patch release 13
Supplementary files format and content: BigWig files

source_name: T-cell

extract_protocol:
For all samples, 1x105 cells were washed in PBS and pelleted. The cell pellet was resuspended in 100μL freezing medium, composed of 10% dimethyl sulfoxide (Sigma, St. Louis, MO, USA) and 90% FBS (Sigma, St. Louis, MO, USA). Then, it was stored at -80°C prior to shipment to CD Genomics.
Nextera kit

treatment_protocol: CART19-28ζ cells from three biological replicates were collected before (baseline) or after chronic stimulation (exhausted) in our in vitro model for CART cell exhaustion. In this model, CART cells were chronically stimulated with JeKo-1 cells.

value: T-cell

value: Exhausted


title: ExhaustedCART_ATAC-seq Biorep2


title: cardiomyocyte,sham, replicate2-61, scRNAseq

department: Department of Cardiovascular Medicine

description:
smartseq2
sham_2.xlsx


title: BaselineCART_ATAC-seq Biorep2

value: Baseline


title: WD, replicate 2, scRNAseq

value: patient with Wilson's disease


title: MoAM WT D4 rep3

value: Monocyte derived alveolar macrophages

value: Influenza A virus


title: WD, replicate 1, scRNAseq


title: MoAM WT D4 rep1


title: cardiomyocyte,sham, replicate2-59, scRNAseq

description:
smartseq2
sham_2.xlsx

value: heart


title: ExhaustedCART_ATAC-seq Biorep1


title: MoAM WT D4 rep2


title: cardiomyocyte,sham, replicate2-58, scRNAseq

description:
smartseq2
sham_2.xlsx


title: HDSA-TGFb-2

data_processing:
Paired-end 75 bp reads of bulk RNA-seq data were aligned to hg19 reference genome (ENSEMBL, version 67) using STAR alignment tool (version 2.7.3a) with default parameters.
Uniquely mapped reads were employed to quantify gene expression using RSEM software (version 1.3.1).2 Transcripts per million mapped reads (TPM) were calculated to estimate the gene expression levels, normalized for sequencing depth.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM counts for each Sample

extract_protocol:
total RNA was purified from the HEK293 cell line using RNeasy RNA isolation Kit (Qiagen) coupled with an on-column DNase I digestion to eliminate residual DNA. The mRNA was purified from 2 μg of total RNA.
libraries for massive parallel sequencing were constructed with NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB). Library quality was assessed with Agilent Bioanalyzer 2100 system. Next-generation sequencing was performed on an Illumina HiSeq 4000 platform.

value: HDSA-TGFb


title: HDSA-TGFb-1


title: MoAM WT D3 rep2


title: cardiomyocyte,sham, replicate2-62, scRNAseq

description:
smartseq2
sham_2.xlsx


title: U3si-SM-2

city: Guangzhou

first: Liang

state: Guangdong

address: 107th Yanjiangxi Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

data_processing:
Base-calling using bcl2fastq2 v2.19.1 with -r 4 -p 16 -w 4  --barcode-mismatches 0
Adaptor contamination was remove from reads (the number of bases contaminated by the adaptor in reads is greater than 5bp. For pair-end sequencing, if one end is contaminated by the adaptor, the Reads at both ends are removed)；Remove low-quality reads (Reads with more than 50% of the total bases are bases with a mass value of Q ≤ 19 . For pair-end sequencing, if one pair is low-quality reads, the both reads will be removed)；Remove the reads with N rate greater than 5%  (For pair-end sequencing, if one pair contains more than 5% N, the both reads will be removed)
Fastq reads were mapped to genome using hisat2 v2.1.0 with default parameters
Reads count of echo gene was calculated using htseq-count v0.6.1 with -t exon -f bam -s no -a 10
Assembly: hg19(ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz)
Supplementary files format and content: excel files include normalize values for each Sample

source_name: bladder

growth_protocol: T24 was cultured in RPMI-1640 (Gibco) and UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1 OD SiRNA was  diluted at a stocking solution of 125 μL in sterile DEPC-treated water, and cells were treated for 48h with 5 μL of SiRNA.

value: bladder

value: bladder cancer cell

value: SLC2A11-MIF knockdown


title: cardiomyocyte,sham, replicate2-57, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Vector-TGFb-2

value: Vector-TGFb


title: cardiomyocyte,sham, replicate2-56, scRNAseq

description:
smartseq2
sham_2.xlsx


title: BaselineCART_ATAC-seq Biorep3


title: U3si-SM-1


title: MoAM WT D3 rep1

value: MoAM WT


title: MI-3

value: infarct zone

value: MI


title: cardiomyocyte,sham, replicate2-55, scRNAseq

description:
smartseq2
sham_2.xlsx

value: 6-8 weeks old

value: sham


title: U3si-Ctrl

value: Negative control


title: cardiomyocyte,sham, replicate2-54, scRNAseq

description:
smartseq2
sham_2.xlsx

value: cardiomyocyte


title: MoAM WT D2 rep3


title: Vector-TGFb-1


title: cardiomyocyte,sham, replicate2-60, scRNAseq

description:
smartseq2
sham_2.xlsx


title: Vector-SB-1

value: Vector-SB