title: Group 3 innate lymphoid cell, Young gut ILC3s rep1, scRNAseq_S-7-2PurifiedWTA

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

institute: zhejiang universiry

description:
BD Rhapsody
Combined_SMK_FKDL202583071-1a_RSEC_ReadsPerCell
for multiple sample

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The FASTQ files were processed using the BD Rhapsody Targeted analysis pipeline v1.9.1 on the Seven Bridges platform (https://www.sevenbridges.com).
First of all, read pairs with low mean base quality scores (less than 20) were removed. The filtered R1 reads were analyzed to identify the cell label sequences and unique molecular identifiers(UMIs). R2 reads were aligned to the mice reference genome(GRCm38) using Bowtie2. Valid reads with the same cell label, the same UMI sequence, and the same gene were collapsed into a single raw molecule. Recursive substation error correction (RSEC) and distribution-based error correction (DBEC) algorithms were applied to correct sequencing and PCR errors of raw UMI counts. The final single-cell expression matrices containing DBEC-adjusted molecules were used for downstream analysis.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Csv files include readcount values for each Sample with different sample tag

source_name: small intestine

extract_protocol:
Small intestinal ILC3s were sorted from siLP of 6-8 weeks-old C57BL/6 mice. All samples were uniformly resuscitated and washed twice by PBS (with 0.1% BSA), then the cells were 1 ml stain buffer (with 0.1% BSA) and counted. The viability of cells in all samples was assessed >80%.
Cells for all samples were labeled with sample tags (BD Mouse Single-Cell Multiplexing Kit, USA), counted, and multiplexed, ready for single-cell capture. Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System (BD, USA), according to the manufacturer's instructions.

value: Group 3 innate lymphoid cell

value: small intestine

value: C57BL/6 mice

tag: age

value: 6-8 weeks-old

tag: sample tag

value: sample tag 4


title: SCHW00120

status: Public on Jun 07 2023

type: SRA

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

library_source: transcriptomic

data_processing:
Sequences were de-multiplexed using bcl2fastq and aligned to mouse mm10  genome (with Cre and tdTomato genes added).
Paired-end reads from Illumina were trimmed for adapters by  cutadapt(v1.15) and aligned to mm9 (MGSCv37, NCBI) by STAR(v2.5.2b, parameters "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix SCHW00296. --outSAMstrandField intronMotif --genomeLoad NoSharedMemory --outSAMattributes NH HI NM MD AS nM XS --outSAMunmapped Within KeepPairs --outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --outReadsUnmapped Fastx").
LiftOver was performed on GENCODE(vM9) gene database (from mm10 to mm9) by CrossMap(v0.1.5) to improve gene annotation.
Aligned reads were then counted by HTSEQ (v 0.6.1p1) for genes annotated in GENCODE database.  Trimmed reads were also run through FastQ Screen(v0.9.5) against Human, Mouse, Adapters, Univec  databases (Dec 2016) to check for contamination and doublets. Samples with larger unique hits to human over  mouse genomes were considered putative doublets and excluded from analysis. We further excluded samples  with less than 1M reads and those that did not express Dbh.
Assembly: mm9
Supplementary files format and content: raw counts table and quality control matrix

molecule: total RNA

organism: Mus musculus

source_name: brain

extract_protocol:
Fresh brain tissue was placed in ice-cold aCSF (2.5 mM KCl, 7 mM MgCl2, 0.5 mM CaCl2, 1.3 mM NaH2PO4, 110 mM choline chloride, 25 mM NaHCO3, 1.3 mM sodium ascorbate, 20 mM glucose, 0.6 mM sodium pyruvate, bubbled in 95% O2 /5%CO2). 200 μm coronal slices that included the LC were collected. Slices were transferred to a 32°C holding chamber containing oxygenated aCSF, where they recovered for at least 1 hour. tdTomato-expressing LC neurons were manually extracted from the slice using glass pipettes pulled from borosilicate glass (World Precision Instruments) to create an ~50 µm tip. The ends of glass pipette tips containing picked cells were snapped into individual wells of a 96 well plate containing 4µl lysis buffer: 0.1µl RNase inhibitor (Thermo Scientific), 0.1µl ERCC RNA spike-in (Invitrogen), 0.02µl 10% Triton (Sigma), 1µl 10mM dNTP (Invitrogen), 0.1µl 100µM dT (IDT; 5'-AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), and 2.68µl H2O.
Samples underwent primer annealing (72℃ for 3min) before placing on ice. Next, 6µl reverse transcription reagent was added to each sample: 0.14µl H2O, 0.25µl RNase inhibitor, 2µl 5X First Strand Buffer (Clontech), 0.5µl 100mM DTT (Invitrogen), 2µl 5M Betaine (Sigma), 0.06µl 1M MgCl2 (Invitrogen), 0.1µl 100µM TSO (Qiagen; 5'-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G), 0.95µl SmartScribe enzyme (Clontech). Samples were incubated at 42℃ for 90min, 70℃ for 5min, then held at 4℃. DNA preamplification solution (15µl) was next added to each sample: 2.1375µl H2O, 12.5µl 2X Kapa HiFi Hot Start Ready Mix (Kapa Biosystems), 0.25µl 10µM IS_PCR Primer (IDT; 5'-AAGCAGTGGTATCAACGCAGAGT), 0.1125µl Lambda Exonuclease (NEB). Samples were incubated at 37℃ for 30min, 95℃ for 3min, 21 cycles of [98℃ for 20s, 67℃ for 15sec, 72℃ for 4min], 72℃ for 5min, and then held at 4℃. DNA cleanup, quantification, dilution, tagmentation, and barcoding were performed by the Hartwell Center at St. Jude Children’s Research Hospital using standard methods.
Smart-seq2

tag: tissue

value: brain

tag: cell type

value: Dbh-Cre; Ai14 Neuron


title: Group 3 innate lymphoid cell, Young gut  LC3s rep2, scRNAseq_Purified

country: China

description:
BD Rhapsody
Combined_Purified-Sample-Tag-Index_FKDL210279193-1a_1_RSEC_MolsPerCell
for multiple sample

library_source: transcriptomic single cell

tag: strain

value: sample tag 12


title: SCHW00113


title: Group 3 innate lymphoid cell, Young gut ILC3s rep1, scRNAseq_S-7-2Purified


title: Group 3 innate lymphoid cell, Young gut  LC3s rep2, scRNAseq_PurfiedWTAIndex


title: SCHW00111


title: sRNA, ndx1-4, rep2

city: Debrecen

first: Lorant

last: Szekvolgyi

address: Egyetem ter 1.

department: Department of Pharmacy

country: Hungary

institute: University of Debrecen

data_processing:
NGS libraries were sequenced (1x50 bp reads) using an Illumina NextSeq 500 instrument.
The results were analysed using the sRNAnalyzer pipeline as follows: Illumina adapters were trimmed by Cutadapt and reads were then size selected in the 19-25 nt range.
Using sRNAnalyzer, size selected reads were aligned to the miRbase database and a recently published comprehensive small RNA locus database.
Differential sRNA expression between Col-0 and ndx1-4 samples was determined by Deseq2 (adjusted p-value < 0.05).
For data visualisation reads were aligned to the A. thaliana reference sequence (TAIR10) using bowtie2. Duplicate reads have not been filtered out. We used deepTools bamCoverage to create RPKM (Reads per Kilobase per Million) normalized coverage files.
Assembly: A. thaliana (TAIR10)
Supplementary files format and content: Coverage data (bigWig) files are RPKM normalized read coverage data of mapped reads.
Supplementary files format and content: Differentially expressed sRNA data (tab-delimited text file) is a result of DESeq2 analysis between Col-0 and ndx1-4 samples. Data table includes count, log2(Fold Change), adjusted p-value of differentially expressed sRNAs.

organism: Arabidopsis thaliana

source_name: flower

growth_protocol: Inflorescence tissues of 5-week-old Col-0 and ndx1-4 flowering plants were collected.

extract_protocol:
Total RNA was purified from Col-0 and ndx1-4 flowers using the phenol-chloroform extraction method. The quality of total RNA samples was checked by an Agilent bioanalyzer (RIN > 9).
Small DNA libraries were prepared according to Illumina’s NEBNext® Multiplex Small RNA Library Prep protocol.

value: flower

tag: developmental stage

tag: ecotype

tag: genotype

value: ndx1-4 mutant


title: sRNA, ndx1-4, rep1


title: sRNA, Col-0, rep2

value: wild type


title: sRNA, Col-0, rep3


title: SCHW00109


title: HCT116.DroshaKO.UT.rep2

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after).  This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Supplementary files format and content: Tab-delimited file with read, seed (bp 2-7), cell viability based on seed, raw read counts for each sample, and putative source based on blast

organism: Homo sapiens

source_name: HCT116 Drosha k.o. uninfected cells

extract_protocol:
Cell lysates were subjected to pull down with a GW182 FLAG-GST- T6B peptide isolated using anti-FLAG M2 Magnetic beads. Bound RNA was extracted using Trizol follwing by ethanol precipitation.
Small RNA-SEQ libraries containing library fragments 140-160 bp in size were generated using Illumina TruSeq small RNA adapters the protocol described in Hafner et al. (2012) Methods 58:164. RNA of 19-35 nt in length was size selected by Urea-PAGE gel extraction after adpater ligation. The final library of ~157bp was size selected on an agarose-TBE gel. Quality of final cDNA was assessed by Agilent Bioanalyzer and DNA concentration determined by Qubit.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: RNA was isolated from cells uninfected or infected with VSVg pseudotyped HIV R9 Env 𝚫iGFP reporter virus after 28hrs

tag: biomaterial provider

value: Korean Collection for Type Cultures (KCTC)

tag: cell line

value: Drosha k.o.

tag: infection

value: Uninfected cells


title: sRNA, Col-0, rep1


title: SCHW00119


title: Group 3 innate lymphoid cell, Cxxc1-deficient  ILC3s rep2, scRNAseq 1

description:
BD Rhapsody
Combined_STIndex417_BKDL202583480-1a_RSEC_MolsPerCell
for multiple sample
sample tag 2
i7  GCTACGCT           i5TATAGCCT
STIndex417_BKDL202583480-1a_Sample_Tag_Calls

extract_protocol:
Small intestinal ILC3s were sorted from siLP of Cxxc1flox/floxRorccre mice. All samples were uniformly resuscitated and washed twice by PBS (with 0.1% BSA), then the cells were 1 ml stain buffer (with 0.1% BSA) and counted. The viability of cells in all samples was assessed >80%.
Cells for all samples were labeled with sample tags (BD Mouse Single-Cell Multiplexing Kit, USA), counted, and multiplexed, ready for single-cell capture. Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System (BD, USA), according to the manufacturer's instructions.

value: Cxxc1flox/floxRorccre mice


title: C57BL.6J_rep1

city: Durham

first: Clare

last: Smith

state: North Carolina

address: 207 Research Drive

department: MGM

institute: Duke University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
100-base paired-end reads were trimmed and aligned to the M. tuberculosis H37Rv genome to identify sites of himar1 insertion. Custom Perl programs available at https://github.com/sassettilab/Bellerose_et_al_mSystems_TnSeq_analyses were used for the read trimming and subsequently to summarize insertion counts at each genomic TA dinucleotide (see subdirectory 'TnSeq_insertion_counts_v6' under the aforementioned Github link).
Insertion mutant counts across all libraries were normalized by beta-geometric correction (DeJesus, M.A., Ambadipudi, C., Baker, R., Sassetti, C., and Ioerger, T.R. (2015). TRANSIT--A Software Tool for Himar1 TnSeq Analysis. PLoS Comput Biol: 11, e1004401), binned by gene, and replicate values for each mouse genotype averaged.
Assembly: NC_018143.2
Supplementary files format and content: Tab-delimited text files generated in the custom data processing pipeline: col 1, genome coordinate; col 2, unique insertion counts
Library strategy: TnSeq

molecule: genomic DNA

organism: Mycobacterium tuberculosis H37Rv

source_name: homogenized mouse spleen

extract_protocol:
Spleens from infected mice were homogenized and approximately 1.0E+06 CFU per mouse was plated on 7H10 agar with 20ug/mL kanamycin. After three weeks of growth, colonies were harvested by scraping, and genomic DNA was extracted as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling, Methods Mol Biol: 1279:79-95.
Libraries were prepared for Illumina sequencing using custom primers as described in Long JE, DeJesus M, Ward D, Baker RE, Ioerger T, Sassetti CM (2015). Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 1279:79-95. In the majority of cases, two replicate mouse libraries were used per genotype. Only a single TnSeq library was obtained for BXD48a and BXD51. Five replicate libraries were obtained for in vitro-grown libraries.

treatment_protocol: Mice were infected with 1.0E+06 CFU of saturated Himar1 transposon mutants delivered via intravenous tail vein injection. At 4 weeks post-infection, mice were euthanized and organs harvested.

tag: h37rv genotype

value: himar1 transposon library

tag: mouse strain

tag: infection length (days)


title: SCHW00107


title: SCHW00108


title: Group 3 innate lymphoid cell, Cxxc1-deficient  ILC3s rep2, scRNAseq 2

description:
BD Rhapsody
Combined_STIndex417_BKDL202583480-1a_RSEC_MolsPerCell
for multiple sample
sample tag 2
i7  CGAGGCTG           i5TATAGCCT
STIndex417_BKDL202583480-1a_Sample_Tag_Calls


title: HCT116.DroshaKO.HIV.rep1

source_name: HCT116 Drosha k.o. VSVg pseudotyped HIV-1 virus infected cells

value: Cells were infected with HIV-1 for 28hrs


title: HCT116.WT.UT.rep2

source_name: HCT116wt uninfected cells

value: wt


title: sRNA, ndx1-4, rep3


title: SCHW00110


title: hy5hyh-UV rep3

city: Bristol

first: Keara

last: Franklin

address: 24 Tyndall Avenue

department: School of Biological Sciences

country: United Kingdom

institute: University of Bristol

data_processing:
Basecalls performed with Illumina RTA 2.4.6
Reads trimmed and filtered with Trimmomatic v0.39 (SLIDINGWINDOW:5:20 MINLEN:50)
Reads were aligned against the A. thaliana TAIR10 genome assembly downloaded from plants.ensembl.org using HISAT2 v2.2.1
Gene count tables were generated with HTSeq-count v0.13.5
Differential gene expression analysis was performed using the R v4.0.3 package DESeq2 v1.30.1, using default settings
Genome_build: TAIR10: GCA_000001735.1
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample

source_name: aerial tissue

growth_protocol: Seeds were sown directly onto a 3:1 mixture of compost and horticultural silver sand. Unless otherwise stated, seeds were stratified for 3 d in darkness at 4 °C before transfer to controlled growth cabinets (Microclima 1600E, Snijder Scientific, The Netherlands) set to 16 h light /8 h dark cycles (R:FR ~ 2.5) at 20 °C and 70% humidity.

extract_protocol:
RNA libraries were prepared for sequencing with the Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina, Inc., San Diego, USA)
RNA libraries were prepared following manufacturer's instructions

treatment_protocol: Ws and hy5/hyh seedlings were grown for 7 d in continuous white light (WL) before transfer to WL, +FR, +UV-B or +FR+UV-B for 4 h.

tag: treatment

value: UV-B

tag: plant line

value: hy5/hyh mutant


title: WS-UV rep3

value: Ws

value: Wassilewskija


title: hy5hyh-WL rep3

value: White light


title: HCT116.DroshaKO.UT.rep1


title: Group 3 innate lymphoid cell, Cxxc1-deficient  ILC3s rep1, scRNAseq 1

description:
BD Rhapsody
_1_Combined_SMK_BKDL202572455-1a_RSEC_MolsPerCell
for multiple sample
sample tag 4
i7  GCTACGCT          i5TATAGCCT
_1_SMK_BKDL202572455-1a_Sample_Tag_Calls

value: Group 3 innate lymphoid cell

value: small intestine

value: 6-8 weeks-old


title: SCHW00104

value: brain

value: Dbh-Cre; Ai14 Neuron


title: Group 3 innate lymphoid cell, Cxxc1-deficient  ILC3s rep1, scRNAseq 2

description:
BD Rhapsody
_1_Combined_SMK_BKDL202572455-1a_RSEC_MolsPerCell
for multiple sample
sample tag 4
i7  CGAGGCTG           i5TATAGCCT
_1_SMK_BKDL202572455-1a_Sample_Tag_Calls


title: HCT116.WT.HIV.rep1

source_name: HCT116wt VSVg pseudotyped HIV-1 virus infected cells

value: Korean Collection for Type Cultures (KCTC)


title: SCHW00105


title: Group 3 innate lymphoid cell, aged gut ILC3s rep1, scRNAseq

description:
BD Rhapsody
for multiple sample
sample tag 6

extract_protocol:
Small intestinal ILC3s were sorted from siLP of aged mice. All samples were uniformly resuscitated and washed twice by PBS (with 0.1% BSA), then the cells were 1 ml stain buffer (with 0.1% BSA) and counted. The viability of cells in all samples was assessed >80%.
Cells for all samples were labeled with sample tags (BD Mouse Single-Cell Multiplexing Kit, USA), counted, and multiplexed, ready for single-cell capture. Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System (BD, USA), according to the manufacturer's instructions.
scRNA-seq (BD Rhapsody)

tag: Sex

value: male


title: WS-FR-UV rep1

value: FR LEDs/ UV-B


title: siRNA-Mettl3+CSE.Input

city: Quanzhou City

first: Yaping

last: Zhang

state: Fujian Province

address: No. 34, Zhongshan North Road

institute: The Second Affiliated Hospital of Fujian Medical University

data_processing:
Clean reads of all libraries were aligned to the reference genome (HG19) by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps.
The result of matching the reads to the genome (bam file) is visualized using IGV software to visually observe the abundance of the reads of each sample at a specific position in the genome.
Assembly: hg19
Supplementary files format and content: excel format
Supplementary files format and content: Number of raw junction read

source_name: 16-HBE cell line

growth_protocol: 16-HBE cells were cultured in Dulbecco’s modified eagle’s medium (Gibco) supplemented with10% fetal bovine serum (Gibco) at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from the two groups of cells by using TRIzol Reagent (Invitrogen). The quality and quantity of total RNA were assessed by using NanoDrop ND-1000 (Thermo Fisher Scientific, MA, USA). The RNA integrity was measured using denaturing Agarose gel electrophoresis. Seq-Star T M poly(A) mRNA Isolation Kit (Arraystar, MD, USA) was used to depurate mRNA from total RNA.
he GenSeq™ m6A-MeRIP Kit (GenSeq Inc., China) was used to perform m6A RNA immunoprecipitation by following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).

treatment_protocol: Cigarette smoke extract (CSE) was prepared as follows: 20 ml of culture medium was bubbled with the mainstream smoke from two cigarettes (Shishi brand). After the pH was adjusted to 7.4, the CSE was sterile-filtered through a 0.22μm filter. The CSE is standardized by measuring the absorbance at a wavelength of 320 nm in freshly prepared for each experiment. This solution was considered to be 100% CSE and diluted with culture medium. Then HBECs were exposed to 5%CSE for 24 h.

tag: antibody

value: 16-HBE cell line

value: human bronchial epithelial cells

value: Mettl3 knockdown

value: 5% cigarette smoke extract，MeRIP


title: SCHW00103


title: WS-WL rep3


title: SCHW00106


title: HCT116.WT.UT.rep1

value: wt

value: Uninfected cells


title: Group 3 innate lymphoid cell, aged gut ILC3s rep2, scRNAseq

description:
BD Rhapsody
for multiple sample
sample tag 12

tag: age


title: SCHW00101

tag: tissue


title: siRNA-Mettl3+CSE.IP

tag: cell type

value: 5% cigarette smoke extract


title: hy5hyh-WL rep1

value: hy5/hyh mutant


title: WS-UV rep1

value: UV-B

value: Ws

value: Wassilewskija


title: CSE.Input

value: WT


title: PTEN-Null_1

city: Philadelphia

first: Irfan

last: Asangani

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina bcl2fastq for demultiplexing to generate fastq files
fastq files were aligned to hg19 reference genome using STAR aligner (2.7.3a) with default parameters
samtools (v1.9) was used to convert SAM to BAM and filter out duplicates and reads q<30
bamCoverage was used to convert Bam to bigwig using â€œ--normalizeUsing CPMâ€
Assembly: mm10, hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: PTEN-null mouse prostate organoids

growth_protocol: MDVR cell lines were grown in the medium supplemented with Enzalutamide.

extract_protocol:
RNA was harvested using miRNeasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA library preparation kit Illumina following manufacturer's protocols.

treatment_protocol: ARD-69 or DT-061 treatments were done at a concentration of 100 nM and 10 uM for12 hours respectivily.

value: PTEN-null mouse prostate organoids

value: prostate

tag: source

value: mouse prostate


title: PTEN-WT-2

source_name: PTEN-wt mouse prostate organoids

value: PTEN-wt mouse prostate organoids


title: SCHW00099

value: brain

value: Dbh-Cre; Ai14 Neuron


title: PTEN-Null_2


title: CSE.IP

value: 16-HBE cell line

value: human bronchial epithelial cells


title: hy5hyh-UV rep2


title: PTEN-WT-1


title: SCHW00098


title: WS-WL rep2

value: White light


title: LR-ROD-9

first: Valentin

last: David

state: Illinois

address: 320 E Superior Street

department: Medicine

institute: Northwestern University

data_processing:
StrandNGS 4.0 was used for alignment and differential expression
Sequenced reads were trimmed for adaptor sequence,  masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Strand NGS 4.0
Genome_build: mm10
Annotation: UCSC Transcripts (2018.02.25)
Reads were filtered using the Filter by Read Metrics filter with the following parameters: Quality threshold >= 20; N's allowed in read <= 0; Number of multiple matches allowed <= 1; Removed non-primary multiply mapped reads; Removed reads that are failing vendor's QC.
Reads were further filtered on read quality metrics using the Filter by Genic Region and we retained only reads mapping the Spliced, Partial Genic, Exonic, Genic.
Strand specific reads: false
Max EM Iterations: 1000
Convergence criterion for EM: 0.001
Normalization Type = Deseq
Threshold for normalization = 1
Baseline type =  median of all samples
Supplementary_files_format_and_content: Matrix table with raw and normalized gene counts for every gene and every sample and differential group expression

source_name: Bone Biopsy

extract_protocol:
We isolated total RNA from  bone using TRI reagent (Waltham, MA, USA) and purified RNA using RNeasy kit (Qiagen, Germantown, MD, USA) and submitted 1 µg of total RNA for sequencing.
Libraries were prepared according to Illumina's instructions, i.e, total RNA library for each individual sample was prepared using the TruSeq Total RNA-Seq Library Preparation Kit (Illumina, San Diego, CA), and the bar-coded cDNA libraries were sequenced for 100 bp single reads using Illumina HiSeq 4000.

value: Bone

tag: age (years)

tag: pathology

value: Chronic Kidney Disease and Low Bone Remodeling (LR) Renal Osteodystrophy (ROD)


title: SCHW00100


title: Fmo5(-/-) KO [20183239L]

city: London

first: Elizabeth

last: Shephard

address: Gower Street

institute: University College London

data_processing:
Demultiplexing of all libraries for each sequencing lane using Illumina bcl2fastq2.17.1.14 software (RAW). Clipping of sequencing adapter remnants from all raw reads (AdapterClipped).
Creation of FastQC report for all FASTQ files.
Supplementary_files_format_and_content: *ReadsPerGene.out.tab; read_counts.xlsx; koVswt.csv

source_name: Liver_Fmo5(-/-) KO

extract_protocol:
Livers were removed, flash frozen on dry ice.
Samples were sent to LGC Genomics GmbH (Germany) for RNA extraction (GEN-9300-840), mRNA library (GEN27009) and NextSeq 500 (1x75bp) 400M single reads (GEN27222)

value: Liver

tag: strain background

tag: genotype


title: LR-ROD-8


title: SCHW00095


title: Fmo5(-/-) KO [20183236L]


title: WS-WL rep1


title: WS-FR rep3

value: FR LEDs/ UV-B


title: LR-ROD-5


title: hy5hyh-FR rep3

value: FR LEDS

value: hy5/hyh mutant


title: Fmo5(-/-) KO [20183237L]


title: SCHW00097


title: WT [20181063L]

value: wild type


title: WT [20181064L]


title: LR-ROD-7


title: LR-ROD-4


title: SCHW00094


title: LR-ROD-6


title: SCHW00092


title: WS-UV rep2

value: UV-B

value: Ws

value: Wassilewskija


title: SCHW00091


title: LR-ROD-3


title: hy5hyh-UV rep1


title: WT [20181060L]


title: hy5hyh-FR rep1


title: 16HBE14o- CFTRlow #12 rep2 [ATAC-seq]

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Raw files were trimmed using Sickle (Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33)
Trimmed reads aligned to the hg19 genome using the BWA aligner (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60).
Aligned reads were marked for duplicates using Picard and coverage tracks were generated using deepTools bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016))
Assembly: hg19 genome
Supplementary files format and content: hg19 aligned IDR ATAC-seq of CFTRhigh or CFTRlow cells (n=4) in bigWig format
Supplementary files format and content: hg19 aligned IDR ATAC-seq of each clonal line (2 passages) in bigWig format

growth_protocol: Cells were grown in DMEM + 10% FBS using standard protocols

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

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

tag: cell line

value: CFTRlow


title: WS-FR-UV rep3


title: SCHW00090


title: SCHW00093


title: hy5hyh-FR rep2


title: SCHW00089


title: 16HBE14o- CFTRlow #12 rep1 [ATAC-seq]


title: LR-ROD-1


title: LR-ROD-2


title: 16HBE14o- CFTRlow #3 rep2 [ATAC-seq]


title: SCHW00085


title: HR-ROD-11

value: Chronic Kidney Disease and High Bone Remodeling (HR) Renal Osteodystrophy (ROD)


title: HR-ROD-10


title: hy5hyh-WL rep2


title: SCHW00084

value: brain


title: HR-ROD-9


title: hy5hyh-FR-UV rep2


title: 16HBE14o- CFTRlow #3 rep1 [ATAC-seq]


title: SCHW00083

value: Dbh-Cre; Ai14 Neuron


title: WS-FR rep1


title: HR-ROD-8


title: hy5hyh-FR-UV rep1


title: 16HBE14o- CFTRhigh #7 rep2 [ATAC-seq]

value: CFTRhigh


title: 16HBE14o- CFTRhigh #4 rep2 [ATAC-seq]

value: human bronchial epithelial cells


title: 16HBE14o- CFTRhigh #7 rep1 [ATAC-seq]


title: SCHW00082


title: HR-ROD-7


title: hy5hyh-FR-UV rep3


title: 16HBE14o- CFTRhigh #4 rep1 [ATAC-seq]


title: SCHW00081


title: WS-FR-UV rep2


title: WS-FR rep2


title: SCHW00079


title: HR-ROD-5


title: SCHW00088


title: 16HBE14o- CFTRlow #12 viewpoint_-20.9kb rep1 [4C-seq]

description: 4C-seq library with the CFTR -20.9 kb region as the viewpoint

data_processing:
library strategy: 4C-seq
Libraries were sequenced on the Nextseq550 machine and demultiplexed using the primer sequences.
4C-seq was quantified and mapped using the pipe4C v1.1 (https://github.com/deLaatLab/pipe4C) processing pipeline using default parameters, aligned to the hg19 genome.
Assembly: hg19
Supplementary files format and content: Aligned 4C-seq of each sample of at a single viewpoint in bigWig format

growth_protocol: Cells were grown in DMEM + 10% FBS using standard methods

extract_protocol:
Nuclei from 1e7 cells grown to confluency were made as per Krijger, P et al, 2020, Methods (PMID: 31351925).
All libraries were constructed with Illumina sequencing adapters as per PMID: 31351925.


title: 16HBE14o- CFTRlow #12 viewpoint_-20.9kb rep2 [4C-seq]


title: LAS_Not-injected-6

city: Raleigh

first: Shelly

middle: Jones

last: Nolin

state: NC

address: 2711 Founders Dr

department: Prestage Dept of Poultry Science

institute: NC State University

data_processing:
CLC Genomics Workbench v11 was used for all sequence processing
Adapters were trimmed and sequences were checked for quality during import into CLC Genomics Workbench v11
Sequences for each sample were mapped to the Galgal6 reference genome (GCA_000002315.5) and counts for each transcript were determined in transcripts per million using the RNA-Seq Analysis tool in CLC Genomics Workbench v11
Assembly: Galgal6: GCA_000002315.5
Supplementary files format and content: text tab delimited files including TPM for each sample

organism: Gallus gallus

source_name: Jeunum

extract_protocol:
RNA was isolated from each jejunum sample using the RNEasy mini kit (Qiagen, Hilden, Germany) following manufacturer protocol
Illumina RNA libraries were constructed following manufacturer protocol

value: Jeunum

tag: genetic line

value: LAS

tag: days post_injection


title: SCHW00077


title: 16HBE14o- CFTRlow #12 viewpoint_+48.9kb rep2 [4C-seq]

description: 4C-seq library with the CFTR +48.9 kb region as the viewpoint


title: HR-ROD-3

value: Bone


title: LAS_Not-injected-4


title: LAS_Not-injected-5


title: HR-ROD-4


title: SCHW00076


title: SCHW00074


title: SCHW00072


title: HR-ROD-1


title: LAS_Not-injected-2


title: HR-ROD-2


title: SCHW00071


title: Healthy-9

value: Healthy


title: 16HBE14o- CFTRlow #3 viewpoint_-20.9kb rep2 [4C-seq]


title: 16HBE14o- CFTRlow #3 viewpoint_-20.9kb rep1 [4C-seq]


title: LAS_Not-injected-1


title: HR-ROD-6


title: 16HBE14o- CFTRlow #3 viewpoint_+48.9kb rep2 [4C-seq]


title: SCHW00070


title: Healthy-8


title: LAS_Injected-6

value: SRBC injected


title: Healthy-7


title: SCHW00065


title: 16HBE14o- CFTRlow #3 viewpoint_+48.9kb rep1 [4C-seq]


title: 16HBE14o- CFTRhigh #7 viewpoint_+-20.9kb rep2 [4C-seq]


title: LAS_Injected-5


title: SCHW00064


title: Healthy-6


title: 16HBE14o- CFTRlow #12 viewpoint_+48.9kb rep1 [4C-seq]


title: LAS_Injected-4


title: LAS_Not-injected-3


title: SCHW00063


title: 16HBE14o- CFTRhigh #7 viewpoint_-20.9kb rep1 [4C-seq]


title: 16HBE14o- CFTRhigh #7 viewpoint_+48.9kb rep2 [4C-seq]


title: SCHW00061


title: Healthy-4


title: LAS_Injected-2


title: 16HBE14o- CFTRhigh #7 viewpoint_+48.9kb rep1 [4C-seq]


title: SCHW00060


title: LAS_Injected-3


title: Healthy-3


title: 16HBE14o- CFTRhigh #4 viewpoint_-20.9kb rep2 [4C-seq]


title: SCHW00059


title: Healthy-2


title: HAS_Not-injected-6

value: HAS


title: LAS_Injected-1


title: 16HBE14o- CFTRhigh #4 viewpoint_-20.9kb rep1 [4C-seq]


title: SCHW00057


title: Healthy-1


title: HAS_Not-injected-5


title: 16HBE14o- CFTRhigh #4 viewpoint_+48.9kb rep2 [4C-seq]


title: Adult intestinal esg+ cells, da knock-down batch1, rep3

city: Colchester

first: Joaquin

last: de Navascues Melero

state: Essex

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

data_processing:
map with `--readFilesCommand zcat --outMultimapperOrder Random --outSAMmultNmax 1 --runMode alignReads --outSAMtype BAM Unsorted --quantMode GeneCounts`
index with `bamtools index -in aligned.bam -out indexed.bam`
sort with `bamtools sort -out sorted.bam -in indexed.bam`
count reads per gene with `featureCounts -T 8 -p -C -F GTF -t exon -g gene_id ...`
Assembly: FB2019_03 Dmel Release 6.28
Supplementary files format and content: .featurecounts files contain the mapping of reads to each gene in plain text (tab-delimited)
Supplementary files format and content: .summary files contain summary statistics of the mapping in plain text

organism: Drosophila melanogaster

source_name: Adult midgut

growth_protocol: Flies maintained at 18ºC in normal food until adulthood.

extract_protocol:
We dissected 100 midguts/genotype in triplicate and for each sample 20,000–40,000 cells were sorted into RNAse-free 1× PBS with 5 mM EDTA. RNA was isolated using the Arcturus PicoPure™ RNA Isolation Kit.
The entire amount of isolated RNA was used as input for RNA-amplification using the Arcturus™ RiboAmp™ HS PLUS Kit. Two hundred nanograms of amplified aRNA was used as input for RNA-Seq library preparation using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Switched to 29ºC in normal food for 2 days prior to dissection.

value: Adult midgut

value: esg-positive cells

value: esg-Gal4, UAS-GFP, tub-Gal80[ts], UAS-da-RNAi

value: temperature switch 18>29C


title: SCHW00056


title: 16HBE14o- CFTRhigh #4 viewpoint_+48.9kb rep1 [4C-seq]


title: Healthy-5


title: HAS_Not-injected-4


title: HAS_Not-injected-3


title: 16HBE14o- viewpoint_-20.9kb [4C-seq]

value: WT


title: Adult intestinal esg+ cells, da knock-down batch1, rep2


title: SCHW00054


title: Adult intestinal esg+ cells, da knock-down batch1, rep1


title: SCHW00052


title: HAS_Not-injected-1


title: Adult intestinal esg+ cells, da overexpression batch1, rep2

value: esg-Gal4, UAS-GFP, tub-Gal80[ts], UAS-da


title: 16HBE14o- viewpoint_+48.9kb [4C-seq]


title: Adult intestinal esg+ cells, da overexpression batch1, rep1


title: HAS_Injected-6


title: NFIX_sh2_Day10_Rep2_RNAseq

city: Boxborough

first: Nisha

last: Rajagopal

state: MA

address: 1069 Liberty Square Road

institute: Syros Pharmaceuticals

data_processing:
Reads were aligned to the hg19 ensemble transcriptome and gene-level counts computed using the RSEM-1.3.0 algorithm
Reads rounded to the nearest integer obtained from the rsem-calculate-expression function of the RSEM algorithm were used as input to the DESEQ2.0 algorithm for calculating differential expression. These rounded read counts are made available as a processed data file

molecule: polyA RNA

source_name: Blood

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN)
20 ng RNA was used for library prep using the SMARTer UltraLow PolyA library kit for Illumina Sequencing (Clontech Laboratories Inc.).

treatment_protocol: BM-derived erythroid progenitor NFIX knockdown cells were differentiated using the three phase EDM.  The differentiation state of the cells was determined by staining the cells with fluorescently conjugated antibodies specific to erythroid surface markers: CD36-FITC (Becton, Dickinson, and Company, 20 µL/test), CD71-APC (Becton, Dickinson, and Company, 20 µL/test) and CD235a-BV421 (Becton, Dickinson, and Company, 5 µL/test).

value: Blood

value: Erythroblast

value: NFIX knockdown


title: SCHW00050

value: brain

value: Dbh-Cre; Ai14 Neuron


title: NFIX_sh1_Day10_Rep2_RNAseq


title: HAS_Injected-5

value: Jeunum


title: Adult intestinal esg+ cells, control batch1, rep3

value: esg-Gal4, UAS-GFP, tub-Gal80[ts]


title: SCHW00051


title: HAS_Injected-4


title: Adult intestinal esg+ cells, control batch1, rep2


title: SCHW00046


title: SCHW00048


title: NFIX_sh2_Day7_Rep2_RNAseq


title: HAS_Injected-3


title: NFIX_sh1_Day7_Rep2_RNAseq


title: SCHW00039


title: HAS_Not-injected-2


title: RNA_5_DMOG

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using STAR version 2.6.1c.
Reads were sorted using samtools v.1.8.
Bigwig files were generated using deeptools bamCoverage version v3.5.0, command –normalizeUsing BPM--binsize 1.
Assembly: GRCh38
Supplementary files format and content: Bigwig files were generated using deeptools bamCoverage version v3.5.0, command –normalizeUsing BPM--binsize 1.

source_name: Primary renal tubular cells

growth_protocol: Primary human tubular cells were isolated from tumor nephrectomy specimens and grown in Dulbecco’s modified Eagle’s medium/Ham’s F-12 supplemented with 2.5% (day 1) or 0% (day 2 onwards) fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, 5 μg/ml insulin, 5 μg/ml transferrin, and 5ng/ml selenium (Sigma), triiodothyronine (T3, Sigma) 10 ng/ml, hydrocortisone 1 mg/ml, epidermal growth factor 100 µg/ml (Peprotech). Epithelial origin was confirmed by immunocytochemistry for N- and E-Cadherin.

extract_protocol:
RNA was isolated using the peqGold total RNA kit (VWR Peqlab, Erlangen, Germany) according to the manufacturer´s protocol.
RNA-seq library preparations were carried out using Illumina protocols and libraries were sequenced on HiSeq 2500 platforms (Illumina).

treatment_protocol: Sub-confluent cell cultures were exposed to 1 mM dimethyloxalylglycine (DMOG, Cayman) for 16h to induce HIF stabilization.

value: 16h DMOG


title: SCHW00055

source_name: brain

extract_protocol:
Fresh brain tissue was placed in ice-cold aCSF (2.5 mM KCl, 7 mM MgCl2, 0.5 mM CaCl2, 1.3 mM NaH2PO4, 110 mM choline chloride, 25 mM NaHCO3, 1.3 mM sodium ascorbate, 20 mM glucose, 0.6 mM sodium pyruvate, bubbled in 95% O2 /5%CO2). 200 μm coronal slices that included the LC were collected. Slices were transferred to a 32°C holding chamber containing oxygenated aCSF, where they recovered for at least 1 hour. tdTomato-expressing LC neurons were manually extracted from the slice using glass pipettes pulled from borosilicate glass (World Precision Instruments) to create an ~50 µm tip. The ends of glass pipette tips containing picked cells were snapped into individual wells of a 96 well plate containing 4µl lysis buffer: 0.1µl RNase inhibitor (Thermo Scientific), 0.1µl ERCC RNA spike-in (Invitrogen), 0.02µl 10% Triton (Sigma), 1µl 10mM dNTP (Invitrogen), 0.1µl 100µM dT (IDT; 5'-AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN), and 2.68µl H2O.
Samples underwent primer annealing (72℃ for 3min) before placing on ice. Next, 6µl reverse transcription reagent was added to each sample: 0.14µl H2O, 0.25µl RNase inhibitor, 2µl 5X First Strand Buffer (Clontech), 0.5µl 100mM DTT (Invitrogen), 2µl 5M Betaine (Sigma), 0.06µl 1M MgCl2 (Invitrogen), 0.1µl 100µM TSO (Qiagen; 5'-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G), 0.95µl SmartScribe enzyme (Clontech). Samples were incubated at 42℃ for 90min, 70℃ for 5min, then held at 4℃. DNA preamplification solution (15µl) was next added to each sample: 2.1375µl H2O, 12.5µl 2X Kapa HiFi Hot Start Ready Mix (Kapa Biosystems), 0.25µl 10µM IS_PCR Primer (IDT; 5'-AAGCAGTGGTATCAACGCAGAGT), 0.1125µl Lambda Exonuclease (NEB). Samples were incubated at 37℃ for 30min, 95℃ for 3min, 21 cycles of [98℃ for 20s, 67℃ for 15sec, 72℃ for 4min], 72℃ for 5min, and then held at 4℃. DNA cleanup, quantification, dilution, tagmentation, and barcoding were performed by the Hartwell Center at St. Jude Children’s Research Hospital using standard methods.
Smart-seq2


title: HAS_Injected-2


title: Control_Day7_Rep2_RNAseq

treatment_protocol: Control BM-derived erythroid progenitor were differentiated using the three phase EDM.  The differentiation state of the cells was determined by staining the cells with fluorescently conjugated antibodies specific to erythroid surface markers: CD36-FITC (Becton, Dickinson, and Company, 20 µL/test), CD71-APC (Becton, Dickinson, and Company, 20 µL/test) and CD235a-BV421 (Becton, Dickinson, and Company, 5 µL/test).


title: RNA_5_ctrl

value: control


title: SCHW00038


title: HAS_Injected-1

value: SRBC injected


title: RNA_4_DMOG


title: NFIX_sh2_Day4_Rep2_RNAseq


title: hippocampus,INS+VD-3

city: Changsha

first: Liang

last: Tang

address: No 1501, Leifeng road

institute: Changsha Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: hippocampus

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.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hippocampus

value: insulin

tag: time

value: Day 56


title: RNA_4_ctrl


title: NFIX_sh1_Day4_Rep2_RNAseq


title: Control_Day10_Rep2_RNAseq


title: RNA_3_DMOG


title: SCHW00035


title: hippocampus,INS+VD-1


title: SCHW00036


title: NFIX_sh2_Day10_Rep1_RNAseq


title: SCHW00034


title: RNA_3_ctrl


title: Adult intestinal esg+ cells, control batch1, rep1

value: Adult midgut

value: esg-positive cells


title: NFIX_sh1_Day10_Rep1_RNAseq


title: RNA_2_DMOG


title: hippocampus,VD-2

value: WT

value: normal saline


title: NFIX_sh2_Day7_Rep1_RNAseq

value: Blood


title: SCHW00033


title: RNA_2_ctrl


title: NFIX_sh1_Day7_Rep1_RNAseq

value: Erythroblast


title: hippocampus,VD-1


title: SCHW00030


title: SCHW00037


title: RNA_1_ctrl


title: Control_Day4_Rep2_RNAseq


title: hippocampus, CK-2


title: hippocampus, CK-3


title: hippocampus,INS+VD-2


title: SCHW00028


title: SCHW00027


title: NFIX_sh1_Day4_Rep1_RNAseq

value: NFIX knockdown


title: hippocampus, CK-1


title: STZ3

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

country: Japan

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

data_processing:
Sequenced reads were mapped to the rat reference genome sequences (Rnor6) using STAR v 2.7.10a (https://github.com/alexdobin/STAR/) and uniquely mapped reads were counted by featureCounts function in the Subread package (https://subread.sourceforge.net).
Assembly: Rnor6
Supplementary files format and content: tab-delimited text files include  gene counts for each Sample

extract_protocol:
Total RNA was extracted from the cortex of kidneys or NRK-52E cells using TRIzol (Life Technologies, Carlsbad, CA) and Direct-zol RNA MiniPrep (Zymo Research, Irvine, CA)
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: STZ groups were treated with 10 mM of STZ for 24 h before RNA extraction.

value: Kidney epithelial cell

value: STZ


title: CB_Population6_Donor2_RNAseq_biorep2

treatment_protocol: BM- and CB-derived erythroid progenitor cells were differentiated using the three phase EDM.  The differentiation state of the cells was determined by staining the cells with fluorescently conjugated antibodies specific to erythroid surface markers: CD36-FITC (Becton, Dickinson, and Company, 20 µL/test), CD71-APC (Becton, Dickinson, and Company, 20 µL/test) and CD235a-BV421 (Becton, Dickinson, and Company, 5 µL/test). The antibody co-stained cells were subjected to FACS (Sony SH800, Sony Biotechnology) and were gated based on differential expression of CD36, CD71 and CD235a on different days of erythroid differentiation.


title: hippocampus,VD-3


title: SCHW00026

data_processing:
Sequences were de-multiplexed using bcl2fastq and aligned to mouse mm10  genome (with Cre and tdTomato genes added).
Paired-end reads from Illumina were trimmed for adapters by  cutadapt(v1.15) and aligned to mm9 (MGSCv37, NCBI) by STAR(v2.5.2b, parameters "--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix SCHW00296. --outSAMstrandField intronMotif --genomeLoad NoSharedMemory --outSAMattributes NH HI NM MD AS nM XS --outSAMunmapped Within KeepPairs --outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --outReadsUnmapped Fastx").
LiftOver was performed on GENCODE(vM9) gene database (from mm10 to mm9) by CrossMap(v0.1.5) to improve gene annotation.
Aligned reads were then counted by HTSEQ (v 0.6.1p1) for genes annotated in GENCODE database.  Trimmed reads were also run through FastQ Screen(v0.9.5) against Human, Mouse, Adapters, Univec  databases (Dec 2016) to check for contamination and doublets. Samples with larger unique hits to human over  mouse genomes were considered putative doublets and excluded from analysis. We further excluded samples  with less than 1M reads and those that did not express Dbh.
Assembly: mm9
Supplementary files format and content: raw counts table and quality control matrix

value: brain

value: Dbh-Cre; Ai14 Neuron


title: 954P4M

city: Meath

last: Mckenna

address: Dunsaney

department: Animal Bioscience

country: Ireland

institute: Teagasc

data_processing:
FASTQC software (v0.11.5) was used to check the quality of the raw sequencing reads.
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.5.1).
STAR software was used to calculate the number of sequenced fragments overlapping all protein-coding genes from the ENSEMBLv88 annotation of the bovine genome. The number of counts of reads mapping to each annotated gene from HTSeq was than collated into a single file and used for subsequent differential gene expression.
DESeq2 was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: zipped fastq files

organism: Bos taurus

source_name: muscle

growth_protocol: This experiment was conducted as part of larger study designed to examine the within-animal repeatability of intake, growth and feed efficiency between the growing and finishing stages of the lifespan of Charolais (CH) and Holstein Friesan (HF) beef steers fed the same diet [4]. Briefly, one hundred and sixty seven cattle comprised of 90 CH and 77 HF were used in the study. Following a dietary adaptation period, individual dry matter intake (DMI) and growth were measured over three 70 d feeding phases. Mean BW (SD) and age (SD) at the start of the feeding phase were 395 kg (37.8) and 283 d (18.3), and 294 kg (42.3) and 306 d (7.7), for CH and HF, respectively. Corresponding BW at the start of phase 3 and phase 4 were, 519 (38.3) and 441 (39.2), and 675 (49.8) and 611 (49.3), respectively. During feeding phases 1 and 3 (high concentrate 1 and 2) steers were individually offered the same concentrates (860 g/kg rolled barley, 60 g/kg soya bean meal, 60 g/kg molasses, and 20 g/kg minerals and vitamins) ad libitum plus a restricted allowance of grass silage daily. Throughout the interim period (Zero grazed grass) they were offered zero-grazed grass (DM 196 g/kg) ad libitum. The grass herbage was harvested (without chopping) twice daily from Lolium perenne dominant swards using a ‘zero-grazer’.

extract_protocol:
Total RNA was isolated from 50mg of biopsy samples using QIAzol (Qiagen, UK). Tissue samples were homogenised in 1mL of QIAzol reagent using a rotor-strator tissue lyser (Qiagen, UK) and chloroform (Sigma-Aldrich Ireland, Dublin, Ireland). RNA was subsequently precipitated and purified using the RNeasy plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA. The quantity of the RNA isolated was determined by measuring the absorbance at 260nm using a Nanordrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA). RNA quality was assessed on the Agilent Bioanalyser 2100 using the RNA 6000 Nano Lab Chip kit (Agilent Technologies Ireland Ltd., Dublin, Ireland). RNA quality was also verified by ensuring all RNA samples had an absorbance (A260/280) of between 1.8 to 2.0 and RIN (RNA integrity number) values of between 8 and 10 were deemed high quality. Any samples that had a (A260/280) absorbance of less than 1.8 were cleaned using Zymo Research RNA clean & concentrator kit (Cambridge Biosciences, UK).  High quality RNA samples were selected for cDNA synthesis.
cDNA libraries were prepared from high quality RNA following the manufacturer’s instructions using the Illumina TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA, USA). For each sample, 1 μg of RNA was used for cDNA library preparation. Briefly, mRNA was purified from total RNA and subsequently fragmented. First strand cDNA was synthesised using Superscript II Reverse Transcriptase (Applied Biosystems Ltd., Life Technologies) followed by second strand synthesis using components of the Illumina TruSeq RNA sample prep kit. Adaptors were ligated to the cDNA which was subsequently enriched by 15 cycles of PCR. Libraries were validated on the Agilent Bioanalyser 2100 using the DNA 1000 Nano Lab Chip kit. cDNA concentration was assessed using Nanordrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and samples with >25ng/μl were deemed suitable for further analysis. Following quality control procedures, individual RNAseq libraries were pooled based on their respective sample-specific 6bp adaptors and sequenced at 50bp/sequence single-end read using and Illumina HiSeq 2500 sequencer.

treatment_protocol: Average daily live weight gain (ADG) during the RFI measurement period for each animal was computed as the coefficient of the linear regression of BW (kg) on time (d) by using the GLM procedure of SAS 9.1 (SAS Inst. INC., Cary, NC). Mid-test metabolic BW (MBW) was represented as BW0.75 35 d before the end of the test which was estimated from the intercept and slope of the regression line. Residual feed intake was calculated for each animal as the difference between actual DMI (Dry matter intake) and expected DMI. Expected DMI was computed for each animal using a multiple regression model, regressing DMI on MBW, ADG and mean lumbar BF change. Animals were ranked within breed and diet and following a power analysis (www.biomath.info/power/ttest.htm) the most extreme animals for high RFI (n=12) and low RFI (n=12) were selected for further analysis.

tag: rfi

value: Lo

tag: diet

tag: breed

value: CH


title: SCHW00032

last: Xu

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hosipital


title: STZ2

tag: treatment


title: 871P4M

value: Hi


title: CB_Population5_Donor2_RNAseq_biorep2


title: 856P4M


title: RNA_1_DMOG

value: 16h DMOG


title: STZ1


title: Dcir-/- osteoclast 83

city: Sendai

first: Tomonori

last: Kaifu

state: Miyagi

address: 1-15-1 Fukumuro Miyagino ku

department: Faculty of Medicine

institute: Tohoku Medicine and Pharmaceutical University

description:
OC83
DcirOC_RNAseq_result.xlsx

data_processing:
The raw sequenceing data were processed using TrimGalore v0.6.6 to remove adapter sequences and low-quality reads.
The processed reads were alined to the mouse genome reference mm10 using hisat2 v2.2.0.
Aligned read counts were caluculated by R package Rsubread v1.32.4.
Assembly: mm10
Supplementary files format and content: An Excel file include differential gene values and p-value.

source_name: Osteoclasts

growth_protocol: Bone marrow cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: Total RNA was harvested using FastGeneTM RNA basic kit (NIPPON Genetics). The quality of RNA was determned by the TapeStation system. 1 mg of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Osteoclasts were induced in the presence of M-CSF (20 ng/ml) and RANKL (100 ng/ml) for 2 days cutlure.

tag: strain

value: Osteoclasts

value: day 4

value: Dcir-/-

value: RANKL stimulation for 2 days


title: CB_Population4_Donor2_RNAseq_biorep2

value: WT


title: SCHW00029

city: Memphis

first: Beisi


title: Dcir-/- osteoclast 22

description:
OC22
DcirOC_RNAseq_result.xlsx


title: NFIX_sh2_Day4_Rep1_RNAseq


title: Ctrl3

value: Control


title: 856P1M


title: 854P1M


title: Dcir-/- osteoclast 21

description:
OC21
DcirOC_RNAseq_result.xlsx


title: Control_Day4_Rep1_RNAseq

value: Blood


title: CB_Population3_Donor2_RNAseq_biorep2

value: Erythroblast


title: BM_Population6_Donor2_RNAseq_biorep2


title: Ctrl2


title: WT osteoclasts 94

description:
WT94
DcirOC_RNAseq_result.xlsx

value: wild type


title: 788P3M

value: ZG


title: Ctrl1

value: Kidney epithelial cell


title: BM_Population5_Donor2_RNAseq_biorep2


title: WT osteoclasts 82

description:
WT82
DcirOC_RNAseq_result.xlsx


title: mesenteric lymph nodes, T1L+T. arnold, rep4

city: PITTSBURGH

first: Reinhard

last: Hinterleitner

address: 5051 Centre Avenue

department: Immunology

institute: University of Pittsburgh

data_processing:
Reads were aligned to mouse reference genome mm10 (GRCm38).
Raw FASTQ files were processed using kallisto (v0.46.0) to obtain abundances (TPM) as well as the counts (Bray et al., 2016).
Sleuth (v0.30.0), an R (v4.2.0)/ Bioconductor package was used to identify differentially expressed transcripts among the groups of interest.
Assembly: mm10
Supplementary files format and content: Excel files include normalized reads

source_name: mesenteric lymph node

extract_protocol:
RNA from mesenteric lymph node was prepared using the RNeasy Mini Kit (Qiagen, 74136)
libraries were prepared using the Illumina TruSeq protocol

value: mesenteric lymph node

value: colonized with 10^6 Tritrichomonas arnold + infected with 10^9 PFU reovirus T1L

value: 48 hours post T1L infection


title: 718P4M

value: Lo

value: HF


title: WT osteoclasts 3

description:
WT3
DcirOC_RNAseq_result.xlsx


title: 581P1M

value: Hi

value: CH


title: mesenteric lymph nodes, T1L+T. arnold, rep3


title: B16F02L1, SX682, TFCP2L1

city: Nashviile

last: Richmond

state: TN

address: 2220 Pierce Avenue

department: Department of Pharmacology and Dermatology

institute: Vanderbilt University School of Medicine

data_processing:
Cutadapt v4.1 was used to trim adapters.
Bowtie2 v2.4.1 was used to map reads to the mouse reference genome.
MACS2 v2.2.7.1 was used to call peaks.
Assembly: mm10
Supplementary files format and content: B16F0_DMSO_TFCP2L1_peaks.xls is an excel file containing peaks information identified in B16F0 cells treated with DMSO that were incubated with anti-TFCP2L1.
Supplementary files format and content: B16F02L1_SX682_TFCP2L1_peaks.xls is an excel file containing peaks information identified in B16F0 cells treated with SX682 that were incubated with anti-TFCP2L1.

source_name: murine melanoma cell line B16F0

growth_protocol: B16F0 cells were cultured overnight with either DMSO or SX-682. Cell extracts were incubated with anti-IgG or anti-TFCP2L1, cross-linked with a reversible cross-linker, and prepared and prepared for ChIP-seq analysis.

extract_protocol:
Next, cells were fixed with fresh formaldehyde at final concentration of 1% for 10 min at room temperature. Glycine was added to final concentration of 0.125 M to quench the reaction. Cells were resuspended at 1x107/ml in sonication buffer (10 mM Tris-HCl pH 8.0, 2 mM EDTA pH 8.0, 1% SDS, with Protease Inhibitor Cocktail (Roche) and PhosSTOP™ Phosphatase Inhibitor Cocktail (Roche) and sonicated for 25-30 sec with Diagenode One sonicator in a 50 ul Bioruptor® One Microfluidic Chip till most DNA fragments were in the range of 200 to 700 bp. After sonication, the lysate was adjusted to RIPA buffer conditions (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, with Protease Inhibitor Cocktail and PhosSTOP™ Phosphatase Inhibitor Cocktail). For each immunoprecipitation, lysate from 2x106 cells and 6 μg of anti-TFCP2L1 antibody (Boster Bio) were used. 6.0 μg of normal rabbit IgG was used as a control.
The final enriched DNA library for each immunoprecipitation was created by PCR with KAPA HiFi HotStart Ready Mix and Nextera custom primers using the optimum number of PCR cycles determined by qPCR.

treatment_protocol: Cells were treated with 5μM SX-682 or DMSO vehicle for 24 hours, collected by trypsinization, and resuspended in PBS.

value: murine melanoma cell line B16F0


title: BM_Population4_Donor2_RNAseq_biorep2


title: BM_Population3_Donor2_RNAseq_biorep2


title: mesenteric lymph nodes, T1L+T. arnold, rep2


title: B16F0, DMSO, TFCP2L1

value: DMSO


title: 571P3M


title: mesenteric lymph nodes, T1L+T. arnold, rep1


title: CB_Population6_Donor1_RNAseq_biorep1


title: B16F0, SX682, igG


title: CB_Population5_Donor1_RNAseq_biorep1


title: 5635P1M


title: CB_Population7_Donor1_RNAseq_biorep1


title: 723P1M


title: B16F10, SX-682 treatment, rep2

data_processing:
Cutadapt (https://github.com/marcelm/cutadapt) was used to trim adapters.
STAR was used to map reads to the mouse reference genome.
DESeq2 was used to detect differential expression between conditions.
Assembly: mm10
Supplementary files format and content: A count table that provides complete data with values for all features and all samples.

source_name: murine melanoma cell line B16F10

extract_protocol:
RNA was extracted from cell cultures using the RNeasy Plus Mini Kit (Cat#74134, Qiagen) per manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: murine melanoma cell line B16F10


title: mesenteric lymph nodes, T1L, rep4

value: WT

value: infected with 10^9 PFU reovirus T1L


title: B16F0, DMSO, IgG


title: CB_Population4_Donor1_RNAseq_biorep1

value: Blood


title: mesenteric lymph nodes, T1L, rep3


title: 5633P3M


title: mesenteric lymph nodes, T1L, rep2


title: CB_Population3_Donor1_RNAseq_biorep1

value: Erythroblast


title: B16F10, SX-682 treatment, rep1


title: 5632P4M


title: 5632P3M


title: B16F10, no treatment, rep2


title: CB_Population2_Donor1_RNAseq_biorep1


title: mesenteric lymph nodes, T. arnold, rep4

value: colonized with 10^6 Tritrichomonas arnold


title: mesenteric lymph nodes, T1L, rep1


title: 5632P1M


title: 5635P3M

value: ZG


title: CB_Population1_Donor1_RNAseq_biorep1


title: BM_Population7_Donor1_RNAseq_biorep1


title: B16F0, SX-682 treatment, rep2


title: mesenteric lymph nodes, T. arnold, rep2


title: B16F10, no treatment, rep1


title: mesenteric lymph nodes, T. arnold, rep3


title: 5617P4M


title: B16F0, SX-682 treatment, rep1


title: 5624P1M


title: 5616P3M


title: mesenteric lymph nodes, T. arnold, rep1


title: BM_Population6_Donor1_RNAseq_biorep1


title: mesenteric lymph nodes, PBS, rep4

value: PBS control


title: BM_Population4_Donor1_RNAseq_biorep1


title: 5613P3M


title: BM_Population5_Donor1_RNAseq_biorep1


title: 5613P1M


title: MelanA, SX-682 treatment, rep2

source_name: murine nontumorigenic cell line MelanA

value: murine nontumorigenic cell line MelanA


title: 5612P4M


title: mesenteric lymph nodes, PBS, rep2

value: mesenteric lymph node


title: MelanA, SX-682 treatment, rep1


title: mesenteric lymph nodes, PBS, rep1

value: 48 hours post T1L infection


title: BM_Population1_Donor1_RNAseq_biorep1


title: 5612P3M

value: Lo


title: 5609P4M

value: HF


title: DC1, T1L+T. arnold, rep4

data_processing:
Libraries were demultiplexed using the NextSeq 2000 Dragen server (v 1.4.1.39716) and BCL Convert (v3.9.3).
Reads were aligned to mouse reference genome mm10 (GRCm38).
Raw FASTQ files were processed using kallisto (v0.46.0) to obtain abundances (TPM) as well as the counts (Bray et al., 2016).
Sleuth (v0.30.0), an R (v4.2.0)/ Bioconductor package was used to identify differentially expressed transcripts among the groups of interest.
Assembly: mm10
Supplementary files format and content: Excel files include DEGs

extract_protocol:
For RNA-sequencing on CD103+ CD11b- CD8a+ mLN DCs, 1,000 CD103+ CD11b- CD8a+ DCs were FACS sorted into a 96-well plate containing 12.5 µl of lysis buffer and cDNA was generated using the Takara Smart-Seq HT Kit (Takara, 634438) following manufactures instructions, with 15 cycles of cDNA amplification.
Samples that passed QC with full length cDNA proceeded to library preparation using Illumina Nextera DNA prep (Illumina, 20018705) with UDI indexes (Illumina, 20027214) added using 8 PCR cycles.

value: dendritic cell (cDC1)

value: colonized with 10^6 Tritrichomonas arnold + infected with 10^9 PFU reovirus T1L


title: MelanA, no treatment, rep2


title: B16F0, no treatment, rep2

value: murine melanoma cell line B16F0


title: MelanA, no treatment, rep1


title: U937/iFIP1, Dox+, 1uM JTE-607, QuantSeq-Pool, read 2

first: Bin

last: Tian

state: Pennsylvania

address: 3601 Spruce Street

institute: The Wistar Institute

description: QuantSeq-Pool read2

data_processing:
QuantSeq FWD or QuantSeq-Pool data were processed according to manufacturer’s recommendation. Briefly, For QuantSeq FWD data, read 1 data were first trimmed by using the BBtools 64 and then mapped to the human genome (hg19) using STAR-2.7.7a 65. The number of reads mapped to each gene was counted by using featureCounts 66. For QuantSeq-Pool data, raw pooled data were first demultiplexed by using the idemux tool, and the read 1 data were then used. The Umi_tools package was used to remove read duplicates based on the location of the alignment and the UMI information. The number of reads mapped to each gene was calculated by using the featureCounts tool
Assembly: hg19
Supplementary files format and content: tab-delimited text file including reads count for each pAs/gene

extract_protocol: Library preparation of total RNA was carried out by using the Lexogen 3’ mRNA-Seq QuantSeq FWD or QuantSeq-Pool kit according to manufacturer’s instructions. Library preparation, quality control, and sequencing were carried out by Ademera Health (South Plainfield, NJ, USA). cDNA libraries were sequenced on an Illumina HiSeq machine (2x150 nt) at Ademera Health.

value: Dox-FIP1-on, 1uM JTE-607


title: 5608P1M

first: Clare

value: Hi


title: DC1, T1L+T. arnold, rep3

value: WT


title: CXCR2 Knockout, rep8

source_name: Tumor

extract_protocol:
RNA was extracted from tumor tissues using the RNeasy Plus Mini Kit (Cat#74134, Qiagen) per manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tumor


title: 5605P3M


title: U937/iFIP1, Dox+, DMSO, QuantSeq-Pool, read 2

description: QuantSeq-Pool read2

value: Dox-FIP1-on, DMSO


title: B16F0, no treatment, rep1


title: CXCR2 Knockout, rep7


title: 5588P4M


title: DC1, T1L+T. arnold, rep2


title: DC1, T1L+T. arnold, rep1


title: mesenteric lymph nodes, PBS, rep3


title: BM_Population3_Donor1_RNAseq_biorep1

value: Blood

value: Erythroblast


title: U937/iFIP1, Dox+, DMSO, QuantSeq-Pool, read 1

description: QuantSeq-Pool read1


title: U937/iFIP1, Dox+, 1uM JTE-607, QuantSeq-Pool, read 1

description: QuantSeq-Pool read1


title: CXCR2 Knockout, rep6


title: BM_Population2_Donor1_RNAseq_biorep1


title: 555P1M

value: CH


title: DC1, T1L, rep3

description:
Table_2_sig_DE_PBS_vs_T1L.xlsx
Table_3_sig_DE_T1L_vs_T_arnold+T1L.xlsx

value: infected with 10^9 PFU reovirus T1L


title: U937/iFIP1, Dox-, 1uM JTE-607, QuantSeq-Pool, read 2

description: QuantSeq-Pool read2

value: Dox-FIP1-off, 1uM JTE-607


title: 545P3M

value: ZG


title: U937/iFIP1, Dox-, 1uM JTE-607, QuantSeq-Pool, read 1

description: QuantSeq-Pool read1


title: DC1, T1L, rep2

value: mesenteric lymph node

value: 48 hours post T1L infection


title: CXCR2 Knockout, rep5


title: 449P1M


title: CXCR2 Knockout, rep2


title: DC1, T. arnold, rep3

value: colonized with 10^6 Tritrichomonas arnold


title: CXCR2 Knockout, rep3


title: U937/iFIP1, Dox-, DMSO, QuantSeq-Pool, read 1

description: QuantSeq-Pool read1

value: Dox-FIP1-off, DMSO


title: DC1, T. arnold, rep2

value: dendritic cell (cDC1)


title: U937/iFIP1, Dox-, DMSO, QuantSeq-Pool, read 2

description: QuantSeq-Pool read2


title: CXCR2 Wild Type, rep6


title: DC1, T. arnold, rep1


title: U937 cells with PMA, DMSO, rep2 QuantSeq

value: PMA + DMSO


title: CXCR2 Wild Type, rep7


title: U937 cells, DMSO, rep2 QuantSeq

value: DMSO


title: CXCR2 Knockout, rep1


title: DC1, T1L, rep1


title: 443P4M

value: Hi


title: 443P1M


title: DC1, PBS, rep3

description:
Table_2_sig_DE_PBS_vs_T1L.xlsx
Table_4_sig_DE_PBS_vs_T_arnold.xlsx

value: WT

value: PBS control


title: U937 cells with PMA, DMSO QuantSeq

data_processing:
QuantSeq FWD data were processed according to manufacturer’s recommendation. Briefly, raw reads were first trimmed by using the BBtools (Bushnell et al., 2017) and then mapped to the human genome (hg19) using STAR-2.7.7a (Dobin et al., 2013). The number of reads mapped to each gene was counted by using featureCounts (Liao et al., 2014).
Assembly: hg19
Supplementary files format and content: tab-delimited text file including reads count for each pAs/gene

extract_protocol: Total cellular RNA was subjected to RNA sequencing by using the QuantSeq FWD kit. Library preparation and sequencing were carried out by Admera Health (South Plainfield, NJ, USA).


title: DC1, PBS, rep4


title: CXCR2 Knockout, rep4

value: Tumor


title: CXCR2 Wild Type, rep5


title: 437P3M


title: DC1, PBS, rep2


title: U937 cells, 1uM JTE-607 QuantSeq

value: 1uM JTE-607


title: 427P3M


title: CXCR2 Wild Type, rep4


title: U937 cells with PMA, 1uM JTE-607 QuantSeq


title: DC1, PBS, rep1


title: CXCR2 Wild Type, rep3


title: U937 cells, DMSO QuantSeq


title: shQSER1-2_P53

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

data_processing:
For the ChIP-seq data, the reads were aligned to the human genome build HG19 using bowtie2 (v 2.3.5.1) allowing uniquely mapping reads only
Peaks were called with Homer(7) (v4.11) (p < 1e-5) and the density tracks were normalized to reads per million (RPM) based on mapping results.
Genome_build: HG19
Supplementary_files_format_and_content: bigwig

source_name: Colorectal

extract_protocol:
ChIP was performed according to the previously published protocol (Guo et al.,2020). Briefly, HCT-116 cells were crosslinked with 1% formaldehyde (sigma) for 10 min and quenched with glycine (sangon biotech) for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of  ProteinA Agarose (ROCHE) and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq™ Universal SYBR® Green Supermix (Bio-Rad) on CFX96 (Bio-Rad). The ChIP-seq sample preparation kit was used to prepare generate ChIP-seq library.
NEBNext® DNA Library Prep Master Mix Set for Illumina

value: QSER1 SH-2

tag: chip antibody

value: P53(Santa Cruz sc-126)


title: 367P4M

value: CH


title: CXCR2 Wild Type, rep2

tag: tissue


title: HepG2 cells, 1uM JTE-607 QuantSeq


title: HepG2 cells, DMSO QuantSeq


title: shQSER1-1_P53

value: QSER1 SH-1


title: 364P1M


title: 322P4M

value: Lo


title: SX-682, rep3

growth_protocol: BrafV600E/PTEN-/- mice were fed with either SX-682 chow (0.756 g/kg of SX-682, Syntrix Pharmaceuticals, Inc) or control chow for two weeks prior to tumor induction via topical administration of 2μl of 5mM 4-HT onto the dorsal skin of 4-week-old mice for three successive days.


title: P53KO_QSER1

value: P53 KO


title: QSER1

value: QSER1 SHC


title: CXCR2 Wild Type, rep1


title: 357P3M

value: ZG


title: SX-682, rep4


title: HeLa cells, 10uM JTE-607 QuantSeq

source_name: HeLa

value: HeLa


title: 419P4M


title: HeLa cells, 1uM JTE-607 QuantSeq


title: P53

value: P53 WT


title: HepG2 cells, 10uM JTE-607 QuantSeq


title: 322P1M


title: SX-682, rep1


title: 318P3M


title: HeLa cells, DMSO QuantSeq


title: 310P4M


title: 449P3M


title: control, rep6


title: U937 cells with PMA, 1uM JTE-607 ChrRNA-seq

data_processing:
chrRNA-seq reads were first trimmed by using the TrimGalore tool for removal of 5’ and 3’ adapter sequences. Trimmed reads were mapped to the human genome (hg19) using STAR-2.7.7a (Dobin et al., 2013). The number of reads mapped to each gene was calculated by using the featureCounts tool (Liao et al., 2014).
Assembly: hg19
Supplementary files format and content: tab-delimited text file including reads count for each pAs/gene

extract_protocol:
Chromatin RNA extraction was carried out as previously described (Chen et al., 2019) with  some modifications. Briefly, cells were seeded in 15-cm dishes and were treated with JTE-607 when cell confluency reached 75-80%. Adherent cells were wash with 10 ml of ice-cold PBS twice, scraped from the dishes, and collected into a 10-ml tube. Suspended cells were collected into a 10-ml tube, centrifuged at 420x g at 4°C for 5 min, and then washed with 10 ml ice-cold PBS twice. After removal of PBS, cells were re-suspended in 4 ml of ice-cold HLB+N buffer, containing 10 mM Tris- HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2 and 0.5% (v/) NP-40, and were left on ice for 5 min. Cells were then underlaid with 1 ml of ice-cold HLB+NS buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% (v/v) NP-40 and 10% (wt/vol) sucrose), and were centrifuged at 420x g at 4°C for 5 min. After careful removal of the supernatant, nuclear pellets were re-suspended in 125 ml of ice-cold NUN1 buffer, containing 20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA, and 50% (v/v) glycerol, followed by addition of 1.2 ml of ice-cold NUN2 buffer, containing 20 mM HEPES-KOH (pH 7.6), 300 mM NaCl, 0.2 mM EDTA, 7.5 mM MgCl2, 1% (v/v) NP-40, and 1 M urea. Samples were vortexed at the maximum speed, followed by incubation on ice for 5 min. Chromatin pellets were collected after centrifugation at 16,000x g at 4°C for 2 min and were re-suspended with 50 ul RNase-free water. The chromatin pellet was dispersed by using a 200 µl tip before chromatin RNA was extracted with 1 ml TRIzol.
Chromatin RNA was subject to ribosomal removal  before cDNA library construction by using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina Sequencing were carried out on an Illumina HiSeq machine at Ademera Health (South Plainfield, NJ, USA).


title: SX-682, rep2


title: 310P3M


title: ancNif Mutant Rep 1

city: Madison

first: Betül

last: Kaçar

state: WI

address: 1550 Linden Dr.

department: Department of Bacteriology

institute: University of Wisconsin-Madison

description: Alternative nifD subunit derived by ancestral sequence reconstruction

data_processing:
Raw FASTQ reads were trimmed using Trimmomatic version 0.3 (49) (default settings except for HEADCROP = 5, LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 3:30, MINLEN = 36).
Trimmed reads were aligned to the A. vinelandii DJ genome sequence (GenBank accession CP001157.1) using bwa-mem v0.7.17 (version 0.7.17-h5bf99c6_8) (50) with default parameters. Alignment files were further processed with Picard-tools v2.26.10 (https://broadinstitute.github.io/picard/) (CleanSAM and AddOrRepleaceReadGroups commands) and samtools v1.2 (51) (sort and index commands).
Paired aligned reads were mapped to gene locations using HTSeq v0.6.0 (52) with default parameters.
The R package edgeR v3.30.3 (53) was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg (54) false discovery rate (FDR) adjusted p-value < 0.05 as a significance threshold.
Raw sequencing reads were normalized using the fragments per kilobase per million mapped reads method (FPKM).
Assembly: CP001157.1
Supplementary files format and content: FPKM-data.txt
Supplementary files format and content: Htseq-counts.txt

organism: Azotobacter vinelandii DJ

source_name: bacteria

growth_protocol: Cells were grown to an OD600 of ~0.7 in Burke's nitrogen free media.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). RNA extracts were assessed on a Nanodrop 2000c (Thermofisher Scientific) and confirmed to contain >2.5 µg of RNA with a purity of A260/280 = 1.8-2.2; A260/230 > 1.8. RNA extracts were stored at -80 °C.
RNA-seq library preparation and sequencing was performed by Novogene. \

tag: cell type

value: bacteria

value: ancNif

value: Diazotrophic growth


title: U937 cells with PMA, DMSO ChrRNA-seq

value: DMSO


title: control, rep5


title: 307P4M


title: U937 cells, 1uM JTE-607 ChrRNA-seq


title: control, rep4


title: control, rep3


title: U937 cells, DMSO ChrRNA-seq


title: 307P3M

value: Hi


title: 307P1M


title: WT Rep 1

description: Wildtype

value: WT


title: ancNif Mutant Rep 3


title: WT Rep 3

description: Wildtype


title: control, rep2

value: Tumor


title: ancNif Mutant Rep 2


title: HepG2 cells, 1uM JTE-607 ChrRNA-seq

value: 1uM JTE-607


title: 2297P4M

value: HF


title: control, rep1


title: 2272P3M


title: Wildtype_VAD_rep5

first: Johannes

last: von Lintig

address: 2109 Adelbert Road

department: Pharmacology

description: Sample WD5

data_processing:
The paired-end reads, provided by the fastq files, were aligned to to GRCm38/mm10 genome (UCSC genome source, 2011) using STAR (version 2.5.3a). An average of 87.4% of reads was uniquely mapped to the reference genome. The correlated annotation file (GTF) was applied and the gene expression level was determined by RSEM (version 1.2.30) quantification. Count normalization and differential gene expression was carried out using DESeq2 version 1.32.0. The Wald test was used for comparisons between treatment groups. To account for multiple testing, the FDR cutoff was set at 0.05. gProfiler was used for Gene Ontology and pathway analyses. An overrepresentation test was applied for significant changes in gene expression.
Assembly: mm10
Supplementary files format and content: comma separated values files include normalized counts produced by DESeq2

growth_protocol: Before weaning (~28 days), the pups were kept with dams maintained on a standard rodent chow diet.

extract_protocol:
RNA was harvested using TRIzol and Rneasy mini plus kit (Qiagen). At least 1 ug of total RNA was used for the construction of sequencing libraries (Novogene).
Library preparation and construction were performed by Novogene.

treatment_protocol: After weaning, Stra6 knockout and WT mice were maintained on a diet deficient (0 IU/g) or sufficient (4 IU/g)  in vitamin A  for 12 weeks

value: diet:Vitamin A deficient diet

value: time_on_diet:12 weeks

tag: tissue type

value: RPE-choroid


title: 2266P4M

value: Lo


title: Wildtype_VAD_rep4

description: Sample WD4


title: HeLa cells, DMSO ChrRNA-seq


title: HepG2 cells, DMSO ChrRNA-seq


title: WT Rep 2

description: Wildtype


title: 3-Mettl3-IgE

type: RNA

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

country: Switzerland

institute: Institute for Research in Biomedicine

description: NanoString nCounter Myeloid Innate Immunity Panel

hyb_protocol: samples were hybridized 16h at 65°C

scan_protocol: Samples were run on a Nanostring Sprint Profiler

data_processing: Raw data was processed with nSolver v4.0 and analyzed according to Advanced Analysis Software guidelines (NanoString Technologies)

label: NanoString nCounter CodeSet

source_name: in vitro cultured primary bone marrow derived mast cells (BMMCs)

label_protocol: 40ng of total RNA were labelled with the nCounter Myeloid Innate Immunity Panel codeset according to manufacturer's protocol

growth_protocol: total bone marrow was isolated from mice and cultured for at least 4 weeks in the presence of Il-3 to trigger in vitro bone marrow derived mast cell differentiation. CRISPR/Cas9-HDR modified cells were zsGreen sorted prior activation

extract_protocol: stimulated or resting samples were resuspended in Trizol

treatment_protocol: cells were left resting or activated for 4h with IgE and antigen complexes.

value: bone marrow derived mast cells

value: IgE-antigen stimulation

tag: crispr/cas9 hdr modified gene

tag: sample type

value: test


title: 2259P1M


title: 3-Kit-US

value: unstimulated

value: Kit

value: control


title: Wildtype_VAD_rep3

description: Sample WD3


title: 3-Mettl3-US


title: 3-Kit-IgE


title: 2251P1M


title: Wildtype_VAD_rep2

description: Sample WD2


title: HeLa cells, 1uM JTE-607 ChrRNA-seq

city: Philadelphia

value: HeLa


title: Cybrid2_J1c

city: Madrid

first: Aurora

middle: Gomez

last: Duran

state: Madrid

address: Maria maeztu

department: Molecular Biomedicine

country: Spain

institute: Centro de Investigaciones Biologicas

description:
28J
HPG_10

data_processing:
Data filtering: seqtk 1.0; Trim-galore 0.3.5; Perl script to remove poly-N tails
Mapping: tophat-2.0.6.Linux_x86_64
Counting reads mapped to genes: BEDTools 2.17.0
Testing for differentially expressed genes: DESeq2 1.0.19
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files Gene count file

source_name: Osteosarcoma

growth_protocol: Growth with DMEM. Subconfluent cells were tripsinised.

extract_protocol:
RNA isolation kit (mirVana™ miRNA Isolation Kit)
Illumina TruSeq mRNA library preparation

treatment_protocol: Cold PBS wash. Twice.

tag: type of tissue

value: Tumour cell line

value: Osteosarcoma 143B

tag: mitochondrial haplogroup


title: Cybrid2_H

description:
613H
HPG_12

tag: cell line

value: H


title: 2242P3M

value: Hi

value: ZG


title: Cybrid1_H

description:
RicH
HPG_11


title: 447P1M

value: CH


title: 2-Mettl3-US


title: Wildtype_VAS_rep5

city: Cleveland

institute: Case Western Reserve University

description: Sample WS5

tag: genotype

value: WT

value: diet:Vitamin A sufficient diet


title: 2220P4M

value: HF


title: Cybrid1_J1c

description:
8J
HPG_9


title: Wildtype_VAD_rep1

description: Sample WD1

value: diet:Vitamin A deficient diet

value: time_on_diet:12 weeks

value: RPE-choroid


title: 2-Mettl3-IgE

value: bone marrow derived mast cells

value: IgE-antigen stimulation

value: test


title: 2-Kit-US

value: unstimulated

value: Kit

value: control


title: Wildtype_VAS_rep4

description: Sample WS4


title: 2-Kit-IgE


title: Cybrid2_Uk

description:
48K
HPG_8

value: Tumour cell line

value: Osteosarcoma 143B

value: Uk


title: Cybrid1_Uk

description:
3K
HPG_7


title: Wildtype_VAS_rep3

description: Sample WS3


title: Cybrid2_J2

description:
137J
HPG_6


title: 2102P1M

value: Lo


title: Wildtype_VAS_rep2

description: Sample WS2


title: 2220P1M


title: 2095P4M


title: 1-Mettl3-US


title: 1-Mettl3-IgE


title: Cybrid1_J2

description:
106J
HPG_5


title: 2095P1M


title: Wildtype_VAS_rep1

description: Sample WS1


title: 2094P3M

value: ZG


title: 2087P3M

value: Hi


title: Stra6_VAD_rep5

description: Sample SD5


title: 2085P3M


title: 1-Kit-US


title: Col0, Treated, 10dai, rep2

city: Birmingham

first: Rory

last: Osborne

address: Edgbaston

institute: University of Birmingham

data_processing:
Reads were trimmed using FASTQC and filtered using default parameters
Trimmed and filtered reads were aligned to the TAIR10 genome using Bowtie2 with default parameters
Read count extraction and normalization were performed using DEseq2
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol® and purified using the Qiagen Rneasy mini kit according to manufacturing guidelines.
RNA libraries for RNA-seq were prepared using the Truseq RNA sample preparation v2 kit (Illumina) according to manufacturing guidelines

value: Root

value: Si treated


title: Col0, Treated, 3dai, rep2


title: 1-Kit-IgE


title: Stra6_VAD_rep3

description: Sample SD3

value: diet:Vitamin A deficient diet


title: Stra6_VAD_rep4

description: Sample SD4

value: time_on_diet:12 weeks


title: 2071P4M

value: HF


title: Stra6_VAD_rep2

description: Sample SD2

value: RPE-choroid


title: Col0, Mock, 10dai, rep2

value: Mock


title: Col0, Mock, 3dai, rep2


title: 2071P1M


title: 2069P3M


title: Col0, Treated, 10dai, rep1


title: THIOxenoHCC_roi24_seg010_HCCandStroma

type: protein

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: protein on FFPE tissue section

hyb_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

data_processing: Raw count data of antibody-captured protein copy numbers in each segment were normalized by scaling with geometric mean of the counts of the housekeeping proteins

label: fluorescent barcode

molecule: protein

treatment_protocol: Mice were treated with vehicle control, THIO, anti-PD-L1+anti-VEGF, or anti-PD-L1+anti-VEGF+THIO and sacrificed at the end of the treatment (n=1 per group).

value: HCC/stromal cells (CD3-/CD45-/PanCK+/-)

value: negative

value: positive and negative areas included as CD3-/CD45-

value: anti-PD-L1 + anti-VEGF + THIO


title: THIOxenoHCC_roi24_seg009_HCCandStroma

description: protein on FFPE tissue section

scan_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: positive


title: THIOxenoHCC_roi24_seg008_HCCandStroma

description: protein on FFPE tissue section

label_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals


title: THIOxenoHCC_roi24_seg012_HCCandStroma

description: protein on FFPE tissue section


title: Stra6_VAS_rep5

description: Sample SS5

value: diet:Vitamin A sufficient diet


title: Stra6_VAD_rep1

description: Sample SD1


title: Stra6_VAS_rep4

description: Sample SS4


title: THIOxenoHCC_roi399_seg007_HCCandStroma

description: protein on FFPE tissue section

value: anti-PD-L1 + anti-VEGF


title: Rho0_143B

description:
Rho0
HPG_1

value: Tumour cell line

value: Osteosarcoma 143B

value: no mtDNA


title: 2069P1M

value: Hi


title: THIOxenoHCC_roi24_seg013_HCCandStroma

description: protein on FFPE tissue section


title: 2068P1M

value: Lo


title: THIOxenoHCC_roi399_seg006_HCCandStroma

description: protein on FFPE tissue section


title: Col0, Mock, 10dai, rep1

value: Root


title: 2065P3M

value: ZG


title: Stra6_VAS_rep2

description: Sample SS2

value: time_on_diet:12 weeks


title: 2065P1M

value: HF


title: Col0, Mock, 3dai, rep1

value: Mock


title: 2064P3M


title: Thymocytes,input

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

data_processing:
bwa was used for alignment to the mm10 genome and to generate sam format
samtools was used to convert to bam format and sort
macs3 was used for peak calling with input DNA as background
Encode blacklist file (https://github.com/Boyle-Lab/Blacklist) was used to remove peaks in problematic regions of the genome
bedtools was used to take intersect between AR antibodies to improve sensitivity and mitigate noise in samples
Assembly: mm10
Supplementary files format and content: Filtered files are in macs narrowPeak format

source_name: Thymocytes

extract_protocol:
∼3 × 10^7 cells were fixed, washed and snap-frozen according to the Cell Fixation protocol from Active Motif (http://www.activemotif.com/documents/1848.pdf)
DNA samples after ChIP were made into libraries with TrueSeq DNA Sample Prep Kit (Illumina) and run on Illumina Hiseq 2500 to generate single end reads.

value: Thymocytes

value: 100nM DHT in DMSO for 4hr


title: THIOxenoHCC_roi16_seg008_HCCandStroma

description: protein on FFPE tissue section

value: HCC/stromal cells (CD3-/CD45-/PanCK+/-)

value: negative

value: positive and negative areas included as CD3-/CD45-

value: THIO


title: THIOxenoHCC_roi399_seg005_HCCandStroma

description: protein on FFPE tissue section

value: anti-PD-L1 + anti-VEGF


title: Thymocytes,AR,Ab1

value: sc13062 (Santa Cruz Biotechnology, Inc)


title: Stra6_VAS_rep1

description: Sample SS1

value: diet:Vitamin A sufficient diet

value: RPE-choroid


title: Male_oil II

city: Charlestown

first: Toshihiro

last: Shioda

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

data_processing:
Paired-end (150 + 150) FASTQ files were subjected to trimGalore pre-processing to remove Illumina adaptor sequences and low quality reads (Q<30).
Trimmed FASTQ files were analyzed using the Bismark toolkit to examine CpG methylation. Bismark aligned FASTQ data to the mm10 mouse reference genome using Bowtie2.
Bismark generated .begGraph files reporting CpG site coordinates and their degree of DNA methylation (0-100%).
CpG sites were classified based on their degree of methylation and linked to known mouse repetitive sequences registered in the RepeatMasker file of mm10.
Assembly: mm10
Supplementary files format and content: BedGraph files include coordinates and methylation of CpG sites.

source_name: embryonic gonad

extract_protocol:
Genomic DNA was isolated from FACS-enriched mouse primordial germ cells (20,000 - 30,000 cells) using AllPrep Micro Kit (QIAGEN) and subjected to bisulfite conversion using EZ DNA Methylation-Gold Kit (Zymo Research) following manurfacturers' instructions.
Illumina libraries were synthesized using Accel-NGS Methyl-seq DNA Library Kit (Swift Biosciences) following manufacturer's instructions.

value: embryonic gonad

value: primordial germ cell

tag: Sex

value: M

value: Exposed to vehicle control


title: Col0, Treated, 3dai, rep1

value: Root

value: Si treated

tag: time


title: Male_low II

value: Exposed to 0.033 mg/kg/day BaP


title: 1961P3M

data_processing:
FASTQC software (v0.11.5) was used to check the quality of the raw sequencing reads.
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.5.1).
STAR software was used to calculate the number of sequenced fragments overlapping all protein-coding genes from the ENSEMBLv88 annotation of the bovine genome. The number of counts of reads mapping to each annotated gene from HTSeq was than collated into a single file and used for subsequent differential gene expression.
DESeq2 was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: zipped fastq files

extract_protocol:
Total RNA was isolated from 50mg of biopsy samples using QIAzol (Qiagen, UK). Tissue samples were homogenised in 1mL of QIAzol reagent using a rotor-strator tissue lyser (Qiagen, UK) and chloroform (Sigma-Aldrich Ireland, Dublin, Ireland). RNA was subsequently precipitated and purified using the RNeasy plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA. The quantity of the RNA isolated was determined by measuring the absorbance at 260nm using a Nanordrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA). RNA quality was assessed on the Agilent Bioanalyser 2100 using the RNA 6000 Nano Lab Chip kit (Agilent Technologies Ireland Ltd., Dublin, Ireland). RNA quality was also verified by ensuring all RNA samples had an absorbance (A260/280) of between 1.8 to 2.0 and RIN (RNA integrity number) values of between 8 and 10 were deemed high quality. Any samples that had a (A260/280) absorbance of less than 1.8 were cleaned using Zymo Research RNA clean & concentrator kit (Cambridge Biosciences, UK).  High quality RNA samples were selected for cDNA synthesis.
cDNA libraries were prepared from high quality RNA following the manufacturer’s instructions using the Illumina TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA, USA). For each sample, 1 μg of RNA was used for cDNA library preparation. Briefly, mRNA was purified from total RNA and subsequently fragmented. First strand cDNA was synthesised using Superscript II Reverse Transcriptase (Applied Biosystems Ltd., Life Technologies) followed by second strand synthesis using components of the Illumina TruSeq RNA sample prep kit. Adaptors were ligated to the cDNA which was subsequently enriched by 15 cycles of PCR. Libraries were validated on the Agilent Bioanalyser 2100 using the DNA 1000 Nano Lab Chip kit. cDNA concentration was assessed using Nanordrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA) and samples with >25ng/μl were deemed suitable for further analysis. Following quality control procedures, individual RNAseq libraries were pooled based on their respective sample-specific 6bp adaptors and sequenced at 50bp/sequence single-end read using and Illumina HiSeq 2500 sequencer.

tag: rfi

value: Lo

value: ZG

value: HF


title: Thymocytes,AR,Ab2

value: Thymocytes

value: sc816 (Santa Cruz Biotechnology, Inc)

value: 100nM DHT in DMSO for 4hr


title: Male_high II

value: Exposed to 2 mg/kg/day BaP


title: THIOxenoHCC_roi16_seg005_HCCandStroma

description: protein on FFPE tissue section

value: HCC/stromal cells (CD3-/CD45-/PanCK+/-)

value: negative

value: positive and negative areas included as CD3-/CD45-

value: THIO


title: Stra6_VAS_rep3

description: Sample SS3

value: diet:Vitamin A sufficient diet

value: time_on_diet:12 weeks

value: RPE-choroid


title: THIOxenoHCC_roi16_seg006_HCCandStroma

description: protein on FFPE tissue section


title: 1920P1M

value: Hi

tag: diet


title: Female_oil II

value: embryonic gonad

value: primordial germ cell

value: F

value: Exposed to vehicle control


title: THIOxenoHCC_roi19_seg004_HCCandStroma

description: protein on FFPE tissue section

value: vehicle control


title: K17

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
RNA-Seq reads were trimmed by cutadapt first, then trimmed read were aligned against mouse genome (mm10) using STAR v2.4.2a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread: featureCount with mouse GENCODE gene annotation (M15).
All gene-level transcript counts were then imported into DESeq2, and normalization method was used to adjust for differences in library size
Assembly: mm10
Supplementary files format and content: xlsx

source_name: AngII/PE treated male

extract_protocol: RNA was harvested using Ambion PureLink RNA minikit, lot 2379554, following manufacturer's protocol

value: Whole LV myocardium

value: WT C57Bl6J/129X1 hybrid

value: AngII/PE infusion for 3 days

value: male

value: 3 days


title: K18


title: THIOxenoHCC_roi16_seg007_HCCandStroma

description: protein on FFPE tissue section

value: HCC/stromal cells (CD3-/CD45-/PanCK+/-)

value: negative


title: THIOxenoHCC_roi19_seg003_HCCandStroma

description: protein on FFPE tissue section

value: positive and negative areas included as CD3-/CD45-


title: 1913P4M

tag: breed

value: HF


title: 2064P1M


title: Female_low II

tag: treatment

value: Exposed to 0.033 mg/kg/day BaP


title: K9

source_name: AngII/PE treated female

value: female


title: 1909P3M

value: Lo

value: ZG


title: THIOxenoHCC_roi19_seg002_HCCandStroma

description: protein on FFPE tissue section


title: 1920P4M


title: Male_oil I

value: embryonic gonad

value: primordial germ cell

value: M

tag: strain


title: 1879P3M

value: Hi

value: CH


title: THIOxenoHCC_roi24_seg012_otherLeukocytes

description: protein on FFPE tissue section

value: Other leukocytes (CD3-/CD45+)

value: positive

value: anti-PD-L1 + anti-VEGF + THIO


title: THIOxenoHCC_roi19_seg001_HCCandStroma

description: protein on FFPE tissue section

value: vehicle control


title: Male_low I


title: Male_high I

value: Exposed to 2 mg/kg/day BaP


title: 1877P1M


title: K15

source_name: Control male

value: Whole LV myocardium

value: WT C57Bl6J/129X1 hybrid

value: Nacl for 3 days

value: male

value: 3 days


title: THIOxenoHCC_roi24_seg009_otherLeukocytes

description: protein on FFPE tissue section

value: negative


title: K4

value: AngII/PE infusion for 3 days


title: THIOxenoHCC_roi24_seg010_otherLeukocytes

description: protein on FFPE tissue section


title: 1844P4M

source_name: muscle

value: Lo


title: K14


title: K8

value: female


title: Female_high II

value: embryonic gonad

value: primordial germ cell

value: F


title: Female_high I


title: K6


title: Female_low I

value: Exposed to 0.033 mg/kg/day BaP


title: K13

source_name: Control female


title: 1843P3M

value: Hi

value: ZG

value: CH


title: 1834P3M


title: K16


title: PCN organoid 2 of 2

city: Houston

first: Jae-Il

last: Park

state: Texas

address: 6565 MD Anderson BLVD

department: Dept. of Experimental Radiation Oncology

institute: M.D. Anderson Cancer Center

description: Multiplexed

data_processing:
The demultiplexing, barcoded processing, and  gene counting were performed using the Cell Ranger ( v6.1.2)
Assembly: GRCm38/mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: esophagus

extract_protocol:
organoids from WT, PC, PN, and PCN were collected 7 days after seeding and digested with 0.05% trypsin-EDTA at 37 ℃ for 30 min.
Each group was tagged with 2 CMO tags from CellPlex kit (10x Genomics). The tagged cells of each group were pooled together with same number of cells after counting cells. cDNA library was prepared with the 10x Genomics 3’ v2 kit.

value: organoid

value: epithelial cell

value: Trp53;Cdkn2a;Notch1 KO


title: K12

value: Whole LV myocardium

value: WT C57Bl6J/129X1 hybrid

value: Nacl for 3 days


title: THIOxenoHCC_roi399_seg005_otherLeukocytes

description: protein on FFPE tissue section

value: Other leukocytes (CD3-/CD45+)

value: negative

value: positive

value: anti-PD-L1 + anti-VEGF


title: THIOxenoHCC_roi399_seg006_otherLeukocytes

description: protein on FFPE tissue section


title: THIOxenoHCC_roi399_seg007_otherLeukocytes

description: protein on FFPE tissue section


title: 1846P1M

city: Meath

last: Mckenna

address: Dunsaney

institute: Teagasc

value: Lo


title: K11

value: female

value: 3 days


title: Female_oil I

value: embryonic gonad

value: primordial germ cell

value: F

value: Exposed to vehicle control


title: 1831P1M

value: CH


title: 1831P3M

value: ZG


title: THIOxenoHCC_roi16_seg008_otherLeukocytes

description: protein on FFPE tissue section

value: THIO


title: THIOxenoHCC_roi24_seg008_otherLeukocytes

description: protein on FFPE tissue section

value: anti-PD-L1 + anti-VEGF + THIO