title: Streptococcus sample at 72 hours [2075_7344_33056_578_Mouse430A+2]


title: Ischemic stroke late_IS6_2

status: Public on Aug 05 2024

type: SRA

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

country: USA

institute: The University of Chicago

library_source: transcriptomic

data_processing:
Raw sequencing QC assessement: FastQC v0.11.9
Adapter trimming: cutadapt 3.2
Alignment: bowtie wrapped in sRNAbench v 1.5
miRNA assembly: sRNAbench v 1.5
Differentially expressed miRNA analysis: DESeq2
Assembly: GENCODE human genome model: GRCh38 v34; mature and hairpin micro RNA: miRBase release 22.1
Supplementary files format and content: tab-delimited text files include sense and anti-sense raw counts values summarized by sRNAbench for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

extract_protocol:
MiRNAs were extracted from the serum samples using QIAseq miRNA Library Kit (QIAGENÒ)
The quality of the samples was ensured using Advanced Analytical Fragment Analyzer. Sample concentration was measured with Qubit Fluorometric Quantitation, Life Technologies. Library preparation was performed according to the library preparation protocol (QIAseq miRNA Library Kit (QIAGEN). Human Brain Total RNA AM7962 (ThermoFisher Scientific) was used as positive control. Sequencing run was performed using Illumina NovaSeq 6000 SP platform using single-end 75-bp reads. Raw sequencing quality was assessed using FastQC.

tag: tissue

value: Serum

tag: disease

value: Ischemic stroke late

tag: Sex

value: male


title: EpSRC4XX_rna

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

description: Single cell RNA-seq tdTomato epithelioid sarcoma

library_source: transcriptomic single cell

data_processing:
Samples were demultiplexed using cellranger mkfastq with bclfastq2.
Samples were aligned and output matrices generated using cellranger count for alignment.
cellranger aggregate for alignment, matrix etc
Assembly: mm10 with appended tdTomato and EGFP sequences
Supplementary files format and content: gene matrices, cell barcode and gene list are included as .mtx, .tsv and .tsv files, respectively

molecule: polyA RNA

organism: Mus musculus

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/LSLtdTomato;Smarcb1FL/FL sarcoma cells endpoint 4

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology.

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium library preparation pipeline and subsequent NGS.
10X Chromium Single Cell 3' v2

treatment_protocol: Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before experments were performed.

tag: cell type

value: Mesenchymal Progenitors

tag: strain

value: Hip

tag: genotype


title: EpSRC3XX_rna

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/LSLtdTomato;Smarcb1FL/FL sarcoma cells endpoint 3

value: Head/ear


title: K562-selinexor-3-cytoplasmic-smallRNA

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

description: cytoplasmic RNA

data_processing:
All samples were trimmed with Trimmomatic (v0.32) to remove low-quality and short reads and aligned to the human genome hg19 using STAR aligner (v 2.7.9a).
For total RNA and polyA RNA, RSEM (v 1.3.1) was used to obtain expected gene counts against the human gene reference Gencode (v 41). Differential expression was determined using DESeq2 and R (v 4.2.0). A gene was considered detected if the TPM (Transcripts Per Million) >1 in at least two replicates of one sample and significantly changed if the adjusted p-value was < 0.05 and fold change >1.5<−1.5.
Alternative splicing bam files with the Gencode v41 annotation file were used as input for rMATS (v4.1.2). Events with |inclusion level difference| > 0.05, P < 0.05 and FDR < 0.05 were identified as significantly differentially expressed AS events
For small RNAseq reads were aligned against human elements in RepBase (v23.08) with STAR (v2.7.9a), and the unmapped output was then mapped against the human genome (hg19), allowing three mismatches and keeping all uniquely aligned reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes the Differentially expressed genes per comparison

growth_protocol: K562 cells were cultured in 10% fetal bovine serum and 1% pencillin/streptomycin at early passages (P1-10) and then treated with either vehicle (DMSO) or 200nM selinexor for 24 hours. After 24 hours, RNA was extracted. For the combination treatment RNA sequencing, cells were treated with either vehicle/DMSO, 200nM eltanexor, 1uM venetoclax, 1uM A1331852, 1uM navitoclax, or the combinations of eltanexor+venetoclax, eltanexor+A1331852, and eltanexor+navitoclax for 24 hours.

extract_protocol:
Total RNA for mRNA sequencing was extracted using QIAGEN RNeasy mini kit. To separate nuclear and cytoplasmic fractions, pellet the cells via centrifugation for 5 minutes at 1500RPM and discard the supernatant. The pellet was then resuspended into 300mL of ice cold 0.25x lysis buffer (Tris-Cl pH 8.0, NaCl, MgCl2, Nonidet P-40). The pellet was kept on ice for two minutes and rotate the tube every 45 seconds to ensure proper lysis followed by centrifugation at highest speed at 4°C for two minutes. After centrifugation, the supernatant was carefully removed and placed in a new tube as this was the cytoplasmic fraction. For the remaining nuclear fraction pellet, 500mL of ice-cold PBS was added and centrifuged at 1500RPM for 5 minutes. The QIAGEN RNeasy mini kit was then used for long RNAs and miRNeasy Tissue/Cells Advanced Micro Kit was used for small RNA extraction.
For mRNA sequencing was Poly(A)-selected and the Illumina libraries were prepared using the TruSeq stranded mRNA Library Preparation kit. For the nuclear cytoplasmic mRNAs, ribsomoal RNA depeletion method with the TruSeq stranded Total RNA library was used with 50 million paired end reads. For the nuclear cytoplasmic small RNAs, the size selection step with the Perkin Elmer Next Flex Small RNA library preparation kit on the Illumina sequencing platform with 50 million single end reads.

tag: cell line

value: chronic myeloid leukemia cells

tag: treatment

value: 200nM selinexor


title: Ischemic stroke late_IS3_2

value: female


title: Streptococcus sample at 72 hours [2075_7344_33055_577_Mouse430A+2]

type: RNA

city: Durham

first: Nicholas

middle: G

last: O'Grady

state: NC

address: 2301 Erwin Rd

department: Department of Medicine, CRU

institute: Duke University

hyb_protocol: Samples were subsequently amplified and hybridized the samples onto Affymetrix murine 430A2.0 microarrays containing 22,690 probes.

scan_protocol: Probe intensities were detected using Axon GenePix 4000B Scanner (Molecular Devices).

data_processing: Image files were generated using Affymetrix GeneChip Command Console software. Data was normalized, robust multichip averaged and converted to an eset using the Affy R package.  Differentially expressed genes were discovered with the limma R package.  Public codebase, relevant to publication, can be found here: https://gitlab.oit.duke.edu/biocat/murine-pneumonia-project

label: biotin

source_name: RNA from murine whole blood

label_protocol: Samples that met the following pre-determined quality checks: 260/280 ratio > 1.8, 260/230 ratio > 1.8, and RNA integrity number >7  were amplified and biotin-labeled using MessageAmp Premier RNA Amplification kit (Ambion)

growth_protocol: Mice were housed in a clean murine housing facility and fed standard chow

extract_protocol: Total RNA was isolated using the Mouse Ribopure Isolation Kit followed by globin mRNA depletion using the GLOBINclear Kit (Ambion).  .

treatment_protocol: Mice were intranasally inoculated with either 50ul S. pneumoniae culture at a dose of 8.7 x 105 CFU, 50 ul M. pneumoniae culture at a dose of 1 x 105 CFU, or 50 ul of PBS as a control for bacterial exposured. Influenza pneumonia was induced using 40 ul of PBS or 40 ul of PBS containing 80 PFU of live influenza virus administered intranasally

value: Female

tag: agent

value: Streptococcus

tag: timepoint in hours

tag: agent_time combined


title: K562-selinexor-2-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: Ischemic stroke late_IS5_2


title: Streptococcus sample at 72 hours [2075_7344_33054_575_Mouse430A+2]


title: Ischemic stroke early_IS3_1

value: Ischemic stroke early


title: EpSRC2XX_rna

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/LSLtdTomato;Smarcb1FL/FL sarcoma cells endpoint 2

value: Head


title: K562-selinexor-1-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: K562 SF3B1 K666N-selinexor-2-nuclear-smallRNA

description: nuclear RNA


title: Streptococcus sample at 72 hours [2075_7344_33021_574_Mouse430A+2]


title: K562-selinexor-3-nuclear-smallRNA

description: nuclear RNA


title: EPSRC1XX_atac

description:
Single cell ATAC-seq tdTomato epithelioid sarcoma
transposase accessible

library_source: genomic single cell

data_processing:
Samples were demultiplexed using cellranger-atac 1.1.0 mkfastq with bcl2fastq.
Samples were aligned and output matrices generated using cellranger-atac 1.1.0 count for alignment and peak calling to cell clustering.
Assembly: mm10
Supplementary files format and content: peak matrices, cell barcode and peak list are included as .mtx, .tsv and .bed files, respectively

molecule: genomic DNA

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/LSLtdTomato;Smarcb1FL/FL sarcoma cells endpoint 1

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium nuclei preperation pipeline.
nuclear lysis protocol: nuclei were lysed for five minutes according to 10x standard protocol and subjected to the transposition reaction followed by library preparation pipeline and subsequent NGS.
Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics; CG000168 Rev B); 2 x 75PE kit to produce 2 X 50 reads

value: Shoulder


title: EpSRC1XX_rna


title: wtMuscleXX_rna

description: Single cell RNA-seq tdTomato MPs quiescent

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Muscle

value: Hindlimb muscle


title: Ischemic stroke early_IS2_1


title: Ischemic stroke late_IS1_2


title: Streptococcus sample at 72 hours [2075_7344_33020_573_Mouse430A+2]


title: Streptococcus sample at 72 hours [2075_7344_33019_572_Mouse430A+2]


title: K562-selinexor-1-nuclear-smallRNA

description: nuclear RNA


title: K562-selinexor-2-nuclear-smallRNA

description: nuclear RNA


title: Ischemic stroke early_IS1_1


title: longcDNA_sonkd_rep1

city: Nijmegen

first: Oscar

last: Garcia-Blay

state: Gelderland

address: Heyendaalseweg 135

department: Biophysical Chemistry

country: Netherlands

institute: Institute for Molecules and Materials (Radboud University)

description: Starting mateial corresponds to total_sonkd_rep1. Raw files are in .fast5, in .tar.gz compression. Processed data file is count table for trascript isoforms. In processed file, first column coresponds to transcript ID, second column corresponds to transcript length, and third column corresponds to the count of reads associated with each transcript in the sample.

data_processing:
total RNA-seq step 1: STAR2.7.11a was utilized to generate an indexed genome reference from GRCm39 mus musculus dna sequences per chromosome.
total RNA-seq step 2: STAR2.7.11a was utilized to align the reads from the .fastq file of each sample to the genome of reference. Output was an unsorted BAM file.
total RNA-seq step 3: BAM files were sorted with samtools
total RNA-seq step 4: SPLICE-q.py was utilized to estimate splicing efficiency of introns. NOTE:  The automatic prefix 'chr' was changed to '' (null) in the SPLICE-q.py file because the chromosome id did not have this prefix in the .bam file
long-read nanopore sequencing step 1: Raw reads were obtained from Nanopore sequencer as .fast5 files
long-read nanopore sequencing step 2: basecalling was performed during sequencing run by the tools provided by Oxford Nanopore.
long-read nanopore sequencing step 3: .fastq files from basecalling were concatenated and  minimap2 was utilized to align the basecalled reads to the transcriptome of reference Mus_musculus.GRCm39.cdna and produce a SAM file.
long-read nanopore sequencing step 4: samtools sort was utilized to produce a sorted BAM file.
long-read nanopore sequencing step 5: samtools index and idxstats were utilized to obtain the results of the alignment in terms of counts per isoform.
Assembly: For total RNA-seq: Mus_musculus.GRCm39.dna.chromosome (1 to X)
Assembly: For long-read nanopore sequencing: Mus_musculus.GRCm39.cds.all
Supplementary files format and content: For total RNA-seq: SPLICEq output (splicing efficiency per intron) in .tsv file.
Supplementary files format and content: For long-read nanopore sequencing: count table of transcripts in .txt file.

source_name: E14 mESCs (129/Ola background)

growth_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 0.5E6 cells in a gelatinized 9.6cm2 well. mESC culture medium  consisted of Dulbecco's Modified Eagle Medium, supplemented with 0.1mM betamercaptoethanol, 1000 U/mL of Penicillin, 0.1 mg/mL of Streptomycin, 1mM of sodium pyruvate , 1000 U/mL of ESGRO recombinant Mouse Leukemia Inhibitory Factor and 15% of ES-qualified heat inactivated Fetal Bovine Serum (FBS)

extract_protocol:
24 hours post-transfection, RNA extraction was performed with TRIzol reagent following instructions of the manufacturer.
RNA amount and quality was assessed with Qubit and BioAnalizer. Rt-qPCR was performed to validate Son KD at the mRNA level. For total RNA-seq: RNA samples were delivered to sequencing company in dry ice. Depletion of rRNA was performed in sequencing location prior to library preparation. For Nanopore cDNA sequencing: library preparation was performed following the instruction provided by the manufacturer (Flow-cell:FLO-MIN106D ;Protocol: cDNA).

treatment_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 1E6 cells in a 25cm2 well. 24 hours post-seeding, transfection of Son siRNA or control siRNA was performed in a total volume of 7 mL of transfection media. Transfection media onsisted on 70% standard complete growth media in absence of antibiotics (Penicillin, Streptomycin) and 30% lipoplex solution with the siRNA. Lipoplex solution was obtained by combining 50% of 5% Lipofectamine2000  in Opti-MEM with 50% of 1mM siRNA in Opti-MEM, and incubating at room temperature for 15 minutes.

value: E14 mESCs (129/Ola background)

value: sonkd


title: longcDNA_control_rep1

value: control


title: Day7_KD_3 [osteogeneic differentiation]

city: Liverpool

first: David

middle: J

last: Wilkinson

address: William Henry Duncan Building, 6 W Derby St

department: Musculoskeletal & Ageing Science

country: United Kingdom

institute: University of Liverpool

data_processing:
Fastq files were trimmed using the settings  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Pseudo-alignment of the fastq files was performed with kallisto (Kallisto-0.48.0).
Gene level quantification and differential expression analysis was performed using the R packages tximport and DESeq2.
Assembly: Ensembl GRCh38 (release 103) transcriptome
Supplementary files format and content: Abundance text files containing the kallisto estimated counts and TPM values for each transcript.

source_name: mesenchymal stem cell

growth_protocol: Mesenchymal stem cells (Lonza) were cultured with MSC growth media (Lonza) supplemented with 5 ng/ml FGF-2 (R&D systems)

extract_protocol:
RNA was harvested by the addition of TRIzol and stored at -80 degrees until required. RNA was extracted using a standard phenol/chloroform extraction and purified using RNeasy minicolumns according to the manufacturer’s instructions (Qiagen, Basel, CH). DNA was removed using an off-column DNase kit (DNA-Free; ThermoFisher)
Sequencing library preparations were performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs, Hitchin, UK) following the manufacturers protocol.

treatment_protocol: MSCs were transfected in 10 cm dishes at a confluency of 40-60%. Cells were transfected with siRNA targetting SERPINA3 or a non-targetting control siRNA (Horizon discovery; both 100 nM) using Dharmafect 1 transfection reagent (Horizon Discovery). After 48 hours, cells were counted and plated. The next day, OsteoMax Media (Merck) was added and cells were cultured for 0, 3 or 7 days prior to RNA extraction.

value: mesenchymal stem cell

value: SERPINA3 knockdown

tag: donor

tag: time

value: Day 7

value: osteogeneic differentiation


title: sknas_TCF4_chip_input

city: Memphis

first: Kevin

last: Freeman

address: 19 S. Manassas

department: GGI

institute: UTHSC

library_source: genomic

data_processing:
BWA-MEM (version 0.7.16a) used to map against hg38
samtools (version 1.7) used to remove duplicate reads
IDR (version 2.0.3) used to call IDR peaks
Assembly: hg38
Supplementary files format and content: narrow Peak file, IDR Peak file

source_name: Human Brain

growth_protocol: Kelly and SK-N-AS neuroblastoma cells were maintained at 37 °C and 5% CO2 and cultured in RPMI, DMEM or EMEM respectively, supplemented with 10% fetal bovine serum.

extract_protocol:
DNA purification was performed with Qiagen MinElute PCR Purification kit . ChIP DNA was used to generate ChIP-Seq libraries.
DNA fragments were repaired, A-tailed and ligated with Illimina adapter. Fragments were size selected using bioanalyzer and then PCR amplified.

treatment_protocol: DNA was sheared by sonication to obtain approximately 500 bp. chromatin fragments were immunoprecipitated using Anti-TCF4 antibody (Abcam, ab217668), or anti-H3K27ac (ab4729).

value: SK-N-AS

tag: antibody

value: input


title: Streptococcus sample at 48 hours [2075_7344_33091_564_Mouse430A+2]


title: Streptococcus sample at 72 hours [2075_7344_33018_570_Mouse430A+2]


title: Streptococcus sample at 48 hours [2075_7344_33090_562_Mouse430A+2]


title: K562 SF3B1 K666N-DMSO-2-cytoplasmic-smallRNA

description: cytoplasmic RNA

value: chronic myeloid leukemia cells

value: Vehicle/DMSO


title: K562 SF3B1 K666N-DMSO-3-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: K562 SF3B1 K666N-DMSO-1-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: Day7_KD_2 [osteogeneic differentiation]


title: Day7_KD_1 [osteogeneic differentiation]


title: K562 SF3B1 K666N-DMSO-3-nuclear-smallRNA

description: nuclear RNA


title: Streptococcus sample at 48 hours [2075_7344_33089_561_Mouse430A+2]

value: Female


title: kelly_TCF4_chip_input

value: KELLY


title: sknas_TCF4_chip_rep1


title: Day7_Control_3 [osteogeneic differentiation]

value: Control siRNA


title: Ischemic stroke late_IS2_2

value: Serum

value: Ischemic stroke late

value: female


title: Streptococcus sample at 48 hours [2075_7344_33049_559_Mouse430A+2]

value: Streptococcus


title: K562 SF3B1 K666N SF3B1 K666N-DMSO-1-nuclear-smallRNA

description: nuclear RNA


title: kelly_TCF4_chip_rep1


title: Streptococcus sample at 48 hours [2075_7344_33088_560_Mouse430A+2]


title: Day7_Control_1 [osteogeneic differentiation]


title: Day7_Control_2 [osteogeneic differentiation]


title: K562-DMSO-3-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: Streptococcus sample at 48 hours [2075_7344_33048_558_Mouse430A+2]


title: kelly_H3k27ac_chip


title: sknas_TCF4_chip_rep2


title: Streptococcus sample at 48 hours [2075_7344_33046_556_Mouse430A+2]


title: Day3_KD_3 [osteogeneic differentiation]

value: Day 3


title: Day3_KD_2 [osteogeneic differentiation]


title: K562-DMSO-2-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: K562-DMSO-1-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: sknas_jq1_trt_3hr_rep3

data_processing:
sequencing data is mapped to respective genome using STAR (version 2.5.3a)
featureCounts (subread version 1.5.1) was used to get gene level quantification
Differential gene expression analysis carried out using DeSeq2
Assembly: hg38
Supplementary files format and content: raw reacounts in csv format

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. On-column DNase treatment was performed
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA. Illumina PE150 technology is employed to sequence the sample

treatment_protocol: Cell line treatment was carried out based on dox-inducible shRNA and JQ1. Kelly and SK-N-AS Dox-inducible shRNA cell lines were established and treated with 1ug/ml doxycycline for 3 days. Kelly and SK-N-AS cells were treated with 1uM JQ1 for 3 hours.

value: JQ1 treated


title: Day3_KD_1 [osteogeneic differentiation]

value: mesenchymal stem cell


title: K562-DMSO-3-nuclear-smallRNA

description: nuclear RNA


title: Streptococcus sample at 48 hours [2075_7344_33045_555_Mouse430A+2]


title: sknas_ctrl_3hr_rep3

value: wild


title: kelly_TCF4_chip_rep2


title: sknas_jq1_trt_3hr_rep2


title: K562-DMSO-2-nuclear-smallRNA

description: nuclear RNA


title: Day3_Control_2 [osteogeneic differentiation]


title: K562-DMSO-1-nuclear-smallRNA

description: nuclear RNA


title: Streptococcus sample at 48 hours [2075_7344_33012_553_Mouse430A+2]


title: Streptococcus sample at 48 hours [2075_7344_33047_557_Mouse430A+2]


title: Streptococcus sample at 48 hours [2075_7344_33011_552_Mouse430A+2]


title: sknas_ctrl_3hr_rep2


title: Day3_Control_1 [osteogeneic differentiation]

value: Day 0


title: 48h-5

city: Shanghai

first: Wangsheng

last: Wang

state: Please Select

address: 845 Lingshan Rd.

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava software used for base calling.
After removing the adaptor sequences and low-quality reads, the clean reads were aligned to human genome (GRCh38, NCBI) using Hisat2 with default options
High-throughput sequencing (HTseq)  was used to get gene counts and reads per kilo base per million mapped reads (RPKM) were used to determine gene expression levels
Differential expression analysis was performed using the DESeq2 algorithm
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene RPKM for every gene and every sample

source_name: placental  trophoblasts

extract_protocol:
Total RNA was extracted from cultured primary placental trophoblasts using Trizol reagent (Life Technologies Inc., Grand Island, NY)
RNA-sequence libraries were constructed using a TruSeq RNA sample preparation kit (Illumina Inc.) following the manufacturer’s protocol.

value: trophoblasts

value: cultrue for 48 hours

value: placenta


title: Day0_KD_3 [osteogeneic differentiation]

value: SERPINA3 knockdown

value: osteogeneic differentiation


title: kelly_H3k27ac_chip_input

value: input


title: sknas_jq1_trt_3hr_rep1

value: SK-N-AS


title: 48h-4


title: sknas_ctrl_3hr_rep1


title: Day0_KD_2 [osteogeneic differentiation]


title: 48h-2


title: Day3_Control_3 [osteogeneic differentiation]

value: Control siRNA


title: Streptococcus sample at 24 hours [2075_7344_33082_544_Mouse430A+2]

value: Female


title: Day0_KD_1 [osteogeneic differentiation]


title: Streptococcus sample at 48 hours [2075_7344_33013_554_Mouse430A+2]


title: imr32_ctrl_3hr_rep3


title: 48h-1


title: Streptococcus sample at 48 hours [2075_7344_33009_550_Mouse430A+2]


title: Day0_Control_3 [osteogeneic differentiation]


title: Streptococcus sample at 24 hours [2075_7344_33081_543_Mouse430A+2]


title: 3h-5

value: cultrue for 3 hours


title: Streptococcus sample at 24 hours [2075_7344_33080_542_Mouse430A+2]


title: imr32_jq1_trt_3hr_rep2


title: Streptococcus sample at 48 hours [2075_7344_33010_551_Mouse430A+2]


title: Day0_Control_1 [osteogeneic differentiation]


title: Streptococcus sample at 24 hours [2075_7344_33036_541_Mouse430A+2]


title: Day0_Control_2 [osteogeneic differentiation]


title: imr32_ctrl_3hr_rep2


title: 3h-4


title: H3K14ac_mst2_CDx2

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs from ChIPseq were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li, H. & Durbin, 2009). Macs2 (Zhang, Y. et al. 2008) was used to process the resulting BAM files to product bedgraphs normalized to input and untagged controls.  Deeptools (Ramirez et al. 2016) bamCoverage was used to generate CPM normalized bedgraphs for input and untagged BAMS.
Assembly: S. pombeV2 reference with the sequence of the full 40 kbmatregion provided on a separate contig (MAT).
Supplementary files format and content: Bedgraph format of read counts normalized to reads per million mapped reads (RPM).

organism: Schizosaccharomyces pombe

source_name: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+  mst2-3xHA-chp1CD-V5-chp1CD::bsdMX

growth_protocol: Growth in YEA at 30°C

extract_protocol:
Cells were crosslinked using 3% PFA at room temperature or 18°C for 30 min. Cells were spun at 3000rpm for 5 min washed and pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 200–700 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

tag: chip antibody

value: Abcam anti-H3K14ac ab52946

tag: growth

value: Growth in YEA 30C

tag: fixation

value: 3% PFA


title: 3h-2

tag: tissue


title: imr32_jq1_trt_3hr_rep1

value: JQ1 treated


title: Day7_KD_3

extract_protocol:
Cartilage pellets were ground in TRIzol Reagent (200 µl; ThermoFisher Scientific) and stored at -80 degrees until required. RNA was extracted using a standard phenol/chloroform extraction and purified using RNeasy minicolumns according to the manufacturer’s instructions (Qiagen, Basel, CH). 3 technical repeats were then pooled per donor to provide sufficient material. DNA was removed using an off-column DNase kit (DNA-Free; ThermoFisher).
Sequencing library preparations were performed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs, Hitchin, UK) following the manufacturers protocol.

treatment_protocol: MSCs were transfected in 10 cm dishes at a confluency of 40-60%. Cells were transfected with siRNA targetting SERPINA3 or a non-targetting control siRNA (Horizon discovery; both 100 nM) using Dharmafect 1 transfection reagent (Horizon Discovery). After 48 hours, cells were counted and pelleted in chondrogenic medium (DMEM supplemented with 100 µg/mL sodium pyruvate (Lonza Biosciences), 10 ng/mL TGFβ3, 100 nM dexamethasone, 1x ITS-1 premix, 40 µg/mL proline, and 25 µg/mL ascorbate-2-phosphate (all from Sigma-Aldrich, Poole, UK). Chondrogenesis pellets were cultured for 0, 3 or 7 days prior to RNA extraction.

value: mesenchymal stem cell

value: Day 7

value: chondrogenic differentiation


title: imr32_jq1_trt_3hr_rep3


title: imr32_ctrl_3hr_rep1

value: wild


title: 3h-1

value: trophoblasts


title: Day3_KD_3

value: Day 3


title: Day0_KD_3

value: SERPINA3 knockdown

value: Day 0


title: H3K9me3_WT3

source_name: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+

value: Abcam anti-H3K9me3 8898


title: kelly_jq1_3hr_trt_rep2

value: KELLY


title: Input_231222


title: Day7_Control_2

value: Control siRNA


title: kelly_jq1_3hr_trt_rep3


title: kelly_jq1_3hr_trt_rep1


title: kelly_ctrl_3hr_rep3


title: Swi6_clr3D232N_snf22Δ_rsc1Δ

source_name: mat1Msmt0 leu1-32 ade6-216 ura4  mat2P(Bg-Bs)::ura4+  clr3 D232N-FLAG::KanMX6  snf22∆::KanMX6  rsc1∆::KanMX6


title: Day0_Control_2


title: H3K14ac_WT


title: Swi6_clr3D232N_rsc1Δ

source_name: mat1Msmt0 leu1-32 ade6-216 ura4DS/E mat2P(Bg-Bs)::ura4+  clr3 D232N-FLAG::KanMX6  rsc1∆::KanMX6


title: Day7_Control_3


title: Swi6_snf22Δ_rsc1Δ

source_name: mat1Msmt0 leu1-32 ade6-216 ura4  mat2P(Bg-Bs)::ura4+  snf22∆::KanMX6  rsc1∆::KanMX6


title: kelly_ctrl_3hr_rep2


title: H3K9me3_mst2_CDx2


title: kelly_ctrl_3hr_rep1


title: Day3_Control_3


title: sknas_sh2_ctrl_rep3

value: SK-N-AS


title: Day0_Control_3


title: sknas_sh2_trt_rep3


title: Swi6_clr3D232N

source_name: mat1Msmt0 leu1-32 ade6-216 ura4DS/E mat2P(Bg-Bs)::ura4+ clr3 D232N-FLAG::KanMX6


title: T-ALL cell_3D_biological rep2

city: Madrid

first: Javier

last: Redondo-Muñoz

state: Madrid

address: Ramiro de Maeztu,9

department: Molecular Biomedicine

country: Spain

institute: CIB-CSIC

hyb_protocol: RNA was hybridized to Clariom™ S Human Array following manufacturer’s instructions in a GeneChip Hybridization Oven 645 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Transcriptome Analysis Console (TAC)

label: Biotin

source_name: Jurkat cells cultured in 3D conditions for 3 hours

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit

growth_protocol: Jurkat cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

extract_protocol: RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.

treatment_protocol: Jurkat cells were cultured in suspension or 3D conditions for 3 hours. For 3D matrix, type I collagen solution from bovine were reconstituted at 1.7 mg/mL in RPMI with 10% FBS and neutralized with 7.5% NaHCO3 and 25 mM Hepes. Cells were added to the collagen solution before polymerization at 37 °C for 1 h. Then, warm RPMI with 10% FBS was added to the matrix and incubated for 2 hours.

value: Jurkat

tag: condition

value: cultured in 3D conditions for 3 hours


title: Day3_Control_2


title: Swi6_WT

value: Growth in YEA 30C


title: T-ALL cell_3D_biological rep1


title: T-ALL cell control_biological rep3

source_name: Jurkat cells control

value: control


title: T-ALL cell_3D_biological rep3


title: T-ALL cell control_biological rep1


title: sknas_sh3_ctrl_rep3


title: Swi6_clr3D232N_snf22Δ

source_name: mat1Msmt0 leu1-32 ade6-216 ura4  mat2P(Bg-Bs)::ura4+  clr3 D232N-FLAG::KanMX6  snf22∆::KanMX6

value: 3% PFA


title: sknas_sh3_trt_rep3

value: Sh3 treated


title: Day3_KD_1

value: mesenchymal stem cell


title: Input_20231013


title: H3K9me3_snf59_CDx2

source_name: mat1Msmt0 leu1-32 ade6-210 ura4  mat2P(Bg-Bs)::ura4+  snf59-3xHA-chp1CD-FLAG-chp1CD::KanMX6


title: Day0_KD_1

value: chondrogenic differentiation


title: Day7_KD_2

value: Day 7


title: T-ALL cell control_biological rep2


title: sknas_sh2_ctrl_rep2

value: wild


title: Streptococcus sample at 24 hours [2075_7344_33035_540_Mouse430A+2]

source_name: RNA from murine whole blood

tag: Sex

value: Female

value: Streptococcus


title: H3K9me3_snf5_CDx2_Rep2

source_name: mat1Msmt0 leu1-32 ade6-210 ura4  mat2P(Bg-Bs)::ura4+  snf5-3xHA-chp1CD-FLAG-chp1CD::KanMX6


title: sknas_sh2_trt_rep2


title: MCF7MS-rep3

city: shenyang

first: wen qian

last: chen

address: 77 Puhe Road

department: College of pharmacy

institute: China Medical University

description: Gene expression in MCF-7 MS

hyb_protocol: Following fragmentation, Cy3-labelled cRNAs were hybridized to GeneChip® Human Transcriptome Array 2.0 for 16 hours at 45°C. After hybridization, microarrays were washed and  dried immediately by brief centrifugation.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “P” were chosen for further data analysis.

source_name: MCF-7 MS

label_protocol: total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

growth_protocol: MCF10A cells were cultured in DMEM supplemented with 10% FBS,1X penicillin-streptomycin and plasmocin prophylactic; MCF7 was maintained in DMEM supplemented with 10% FBS and 0.01 mg/ml insulin, 1 X penicillin-streptomycin and plasmocin prophylactic; MCF7 MS were maintained in DMEM‐F12 supplemented with 2% B27, 20 ng/ml human recombinant EGF, 10 ng/ml human recombinant basic FGF.

extract_protocol: Total RNAs were isolated from the whole cells with TRIzol reagent according to the manufacturer’s instructions.

treatment_protocol: Without special treatment

value: MCF-7 MS

tag: cell type

value: Breast cancer cells


title: MCF7MS-rep2

description: Gene expression in MCF-7 MS

scan_protocol: The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).


title: Day7_KD_1

value: SERPINA3 knockdown


title: MCF7MS-rep1

description: Gene expression in MCF-7 MS


title: MCF7_rep3

description: Gene expression in MCF-7


title: H3K9me3_snf5_CDx2_Rep1

tag: strain

value: Abcam anti-H3K9me3 8898


title: sknas_sh3_trt_rep2

value: SK-N-AS


title: MCF7_rep2

description: Gene expression in MCF-7


title: Day3_KD_2

tag: genotype

value: Day 3


title: Day0_KD_2

value: Day 0


title: H3K9me3_WT2

value: Growth in YEA 30C


title: sknas_sh2_ctrl_rep1

tag: cell line


title: smallRNA_KK_RS_2

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
Trim_galore removes adapters and low-quality reads
Mapping to the mouse genome(mm10)
Genes, transcripts or PiRNA quantification
Assembly: mm10
Supplementary files format and content: Txt files of genes, transcripts or PiRNA quantification

source_name: Testis

extract_protocol:
The total RNA was isolated from testicular enriched fractions of pachytene spermatocytes and round spermatids using Trizol (Invitrogen) following manufacturers’ protocol.1 ug of total RNA was used for the construction of RNA sequencing libraries.25 ng CB RNA was used for the construction of sequencing librarie.200 ng total RNA was used for the construction of small RNA sequencing libraries.
RNA libraries for RNA-seq were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina®  in accordance with the manufacturer's recommendations. The total RNA from CB was utilized for strand-specific library preparation without polyA selection or ribosome depletion using the Hieff NGS ®Ultima Dual-mode RNA Library Prep Kit for Illumina®.The small RNA libraries were prepared using the MGIEasy Small RNA Library Prep Kit.

value: Testis

value: Germ cells

value: Round spermatids

value: DDX4 homozygous knock-in

tag: treatment

value: The cells from the testes used two-step digestion method.


title: smallRNA_WK_RS_2

value: DDX4 heterozygous knock-in


title: H3K9me3_clr3Δ_snf22Δ_rsc1Δ

source_name: mat1Msmt0 leu1-32 ade6-216 ura4  mat2P(Bg-Bs)::ura4+  clr3∆::KanMX6  snf22∆::KanMX6  rsc1∆::KanMX6

value: 3% PFA


title: sknas_sh3_ctrl_rep2

source_name: Human Brain

value: wild


title: Day3_Control_1

source_name: mesenchymal stem cell

value: mesenchymal stem cell

value: Control siRNA

value: chondrogenic differentiation


title: sknas_sh2_trt_rep1


title: MCF7_rep1

description: Gene expression in MCF-7

value: Breast cancer cells


title: Day0_Control_1


title: smallRNA_KK_RS_1


title: smallRNA_WK_RS_1


title: MCF-10A_rep1

description: Gene expression in MCF10A


title: H3K9me3_clr3Δ

source_name: mat1Msmt0 leu1-32 ade6-210 ura4DS/E mat2P(Bg-Bs)::ura4+ clr3∆::KanMX6

value: Abcam anti-H3K9me3 8898


title: sknas_sh3_ctrl_rep1

value: SK-N-AS


title: H3K9me3_clr3D232N_snf22Δ_rsc1Δ


title: Day7_Control_1

value: Day 7


title: subpial5

city: Groningen

first: Astrid

last: Alsema

address: Antonius Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

institute: University Medical Center Groningen

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): CGTCAAGGGC,TAGGTCACTC,GAGTGACCTA
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-B12

data_processing:
Fastq files of samples that were sequenced multiple times were appended using SpaceRanger (v.1.2.0).
SpaceRanger (v.1.2.0) with default settings was used to further preprocess the data (deduplications, alignments, creating gene counts and aligning to brightfield images of H&E stained sections).
Data is loaded into R using Seurat::Load10X_Spatial()
Assembly: GRCh38
Supplementary files format and content: Spatial information is provided in the directory "spatial", including tissue_positions_list as csv and tissue images as png. For documentation please refer to: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/images. Processed gene count tables are provided as filtered_feature_bc_matrix.h5

source_name: brain

extract_protocol:
Brightfield images of H&E stained tissue were taken using TissueFaxs (Zeiss AxioObserver Z1 microscope, 20x objective). Manual alignment of fiducial marker spots was done using the Visium Manual Alignment wizard from the SpaceRanger pipeline, which creates the json file provided with the raw data (for documentation please refer to https://support.10xgenomics.com/spatial-gene-expression/software/visualization/latest/alignment)
RNA was extracted following the Visium Spatial Gene Expression User Guide (cat# CG000239 Rev A, 10x Genomics)
Sequencing libraries were generated following the Visium Spatial Gene Expression User Guide (cat# CG000239 Rev A, 10x Genomics)
Paired-end sequencing was performed using Illumina NextSeq 500 Sequencing System with NextSeq 500/550 High Output Kit v2.5 on a 150 bp high output flow cell.

value: grey matter

tag: disease state

value: multiple sclerosis

tag: sn_number spatial transcriptomics slide

tag: capture area spatial transcriptomic slide


title: H3K9me3_snf22Δ_rsc1Δ

value: Growth in YEA 30C


title: subpial4

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): ATGGCTTGTG,GAATGTTGTG,CACAACATTC
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C3


title: H3K9me3_clr3D232N_rsc1Δ


title: smallRNA_WT_RS_2

value: Testis

value: Germ cells

value: WT


title: kelly_sh2_ctrl_rep3

value: KELLY


title: smallRNA_WT_RS_1

value: Round spermatids

value: The cells from the testes used two-step digestion method.


title: H3K9me3_clr3D232N_snf22Δ

value: 3% PFA


title: smallRNA_KK_PS_2

value: pachytene spermatocytes

value: DDX4 homozygous knock-in


title: subpial3

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): GCACTGAGAA,TATGCGTGAA,TTCACGCATA
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-B8


title: kelly_sh2_trt_rep3


title: H3K9me3_clr3D232N


title: kelly_sh3_trt_rep3

value: Sh3 treated


title: Input_231017

source_name: mat1Msmt0 leu1-32 ade6-210 ura4 mat2P(Bg-Bs)::ura4+


title: subpial2

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): TCTTACTTGC,TGACCTCTAG,CTAGAGGTCA
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-B11


title: NAGM3

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): AATGCCATGA,TACGTAATGC,GCATTACGTA
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-B6


title: smallRNA_WK_PS_1

value: DDX4 heterozygous knock-in


title: kelly_sh3_ctrl_rep3

value: wild


title: H3K9me3_WT1

value: Abcam anti-H3K9me3 8898


title: subpial1

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): GCCTTCGGTA,CCAACGATTT,AAATCGTTGG
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-B7


title: smallRNA_KK_PS_1


title: sknas_sh3_trt_rep1

value: SK-N-AS


title: him-8, early embryo, rep3

city: Ann Arbor

first: Gyorgyi

last: Csankovszki

state: MI

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

description:
8125-EJ-6
fpkm_him8_ee
deseq2_him8vsWT_ee.txt

data_processing:
The reads were trimmed using CutAdapt v2.3.FastQC v0.11.8 was used to ensure the quality of data.Reads were mapped to the reference genome WBcel235 and read counts were generated using Salmon v1.9.0. Differential gene expression analysis was performed using DESeq2 v1.42.0. Downstream analyses were performed using R scripts and packages.
Assembly: WS235
Supplementary files format and content: tab-delimited text files with FPKM values and DESeq2 results

organism: Caenorhabditis elegans

source_name: him-8 early embryo

growth_protocol: Embryo samples: synchronized young adult worms were bleached to isolate early embryos. L1 larval samples: Worms were synchronized by bleaching young adult worms to isolate embryos that were allowed to hatch overnight in M9. Newly hatched L1 larval worms were plated and grown for 3 hours on HGM plates with NA22.

extract_protocol:
Packed embryos or L1 larvae were resuspended in TRIzol. RNA was extracted and purified using the Qiagen RNeasy kit with on-column DNAse digestion.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L), and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6448S) were used for library prep.The mRNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3' ends of the cDNA were then adenylated and adapters were ligated. The products were purified and enriched by PCR to create the final cDNA library.

treatment_protocol: Worms grown under standard conditions

tag: developmental stage

value: early embryo


title: kelly_sh2_ctrl_rep2


title: NAGM2

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): GCCCGATGGA,AATCGTCTAG,CTAGACGATT
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-B10

value: grey matter

value: multiple sclerosis


title: NAGM1

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): CAATCCCGAC,CCGAGTAGTA,TACTACTCGG
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C2


title: smallRNA_WT_PS_1

value: Testis


title: smallRNA_WT_PS_2

value: Germ cells


title: kelly_sh2_trt_rep2


title: NAWM3

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): CGAAGTATAC,GAACTTGGAG,CTCCAAGTTC
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-A8

value: white matter


title: him-8, early embryo, rep1

description:
8125-EJ-4
fpkm_him8_ee
deseq2_him8vsWT_ee.txt


title: kelly_sh3_ctrl_rep2

value: KELLY


title: kelly_sh3_trt_rep2


title: him-8, early embryo, rep2

description:
8125-EJ-5
fpkm_him8_ee
deseq2_him8vsWT_ee.txt


title: NAWM2

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): TCCCAAGGGT,TACTACCTTT,AAAGGTAGTA
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-A7


title: Mutant fourth leaves,1-month-old,H3K9ac

city: Gif-sur-Yvette

first: Xiaoning

last: HE

address: 630 Rue Noetzlin

country: France

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of M82 V1.0 genome.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with MACS3.0.0a6  with the command "macs3 callpeak -t sample.bam -c Input.bam -g 829069930 -q 0.05  -B -n --outdir "
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: M82 V1.0
Supplementary files format and content: bigWig, broadPeak

organism: Solanum lycopersicum

source_name: 1-month-old leaves

growth_protocol: M82 and ddm1 seeds were germinated on soil and plants were grown in growth chamber at 24°C with a 16/8h light and dark period

extract_protocol:
ChIP-seq assays were performed according to Ramirez-Prado et al. (Ramirez-Prado et al, 2021) with extra modifications to the chromatin extraction step cross-linked plants were ground using gentleMACS (Miltenyi Biotec) with the 4C program in an extraction buffer (50mM HEPES-KOH pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS) containing protease inhibitors. The mixture was filtered through a 50µm filter and left on ice for 10 minutes. After centrifuge for 10 minutes at 1500g at 4°C, the supernatant was removed and the pellet was resuspended in sonication buffer (50mM HEPES KOH pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.2% SDS) containing protease inhibitors. 4ug of anti-H3K9me2 (Abcam, ab1220), anti-H3K27me1 (Millipore, 07–448), and anti-H3K27me3 (Millipore, 07-449) antibodies were used.
ChIP-seq libraries were prepared from 10 ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: 1-month-old leaves

value: ddm1 mutant


title: WT_3, early embryo, rep3

description:
8125-EJ-3
fpkm_him8_ee
deseq2_him8vsWT_ee.txt

source_name: WT control for him-8 early embryo

value: WT


title: Mutant fourth leaves,1-month-old,H3K27me3,rep2


title: kelly_sh2_ctrl_rep1


title: smallRNA_WK_PS_2

value: pachytene spermatocytes

value: The cells from the testes used two-step digestion method.


title: WT_3, early embryo, rep2

description:
8125-EJ-2
fpkm_him8_ee
deseq2_him8vsWT_ee.txt


title: act/inact6

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): ATGGGTGAAA,CTTGGGAATT,AATTCCCAAG
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C11


title: WT fourth leaves, 1-month-old, rep2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using Hisat2.2.1 aligner with the following setting "--rna-strandness R" against the M82 V1.0 genome.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30 "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m and samtools markdup -r "
Counts reads:Count how many reads map to genomic features with FeatureCounts with the command "featureCounts -F GTF -t exon -g gene_id -a annotation.gff -T 8 -M -O -s 2 -Q 30 -o Count_reads_to_gene.txt input.bams"
Assembly: M82 V1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted from the fourth leaves of 1-month-old plants with Nucleospin RNA kit (Macherey-Nagel), according to the manufacturer’s instructions.
RNA-seq libraries were prepared from 2 μg of total RNA using NEBNext Ultra II Directional RNA library Preparation Kit (NEB) according to the manufacturer’s instructions for the poly(A) mRNA workflow


title: WT_3, early embryo, rep1

description:
8125-EJ-1
fpkm_him8_ee
deseq2_him8vsWT_ee.txt


title: kelly_sh2_trt_rep1


title: WT fourth leaves,1-month-old,H3K9ac


title: xol-1, L1, rep3

description:
4818-EJ-12
fpkm_xol_l1
deseq2_xol1vsWT_l1.txt

source_name: xol-1 L1


title: WT fourth leaves, 1-month-old, rep1


title: kelly_sh3_ctrl_rep1


title: kelly_sh3_trt_rep1

value: Sh3 treated


title: NAWM1

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): CTCTAGCGAG,TATCTTCATC,GATGAAGATA
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-A4


title: act/inact4

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): TCGTCAAGAT,GCAACTCAGG,CCTGAGTTGC
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C12


title: Mutant fourth leaves,1-month-old,rep2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using Hisat2.2.1 aligner with the following setting "--rna-strandness R" against the M82 V1.0 genome.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Counts reads:Count how many reads map to genomic features with FeatureCounts with the command "featureCounts -F GTF -t exon -g gene_id -a annotation.gff -T 8 -M -O -s 2 -Q 30 -o Count_reads_to_gene.txt input.bams"
Assembly: M82 V1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample


title: xol-1, L1, rep1

description:
4818-EJ-9
fpkm_xol_l1
deseq2_xol1vsWT_l1.txt


title: Mutant fourth leaves,1-month-old,rep1


title: WT_2, L1, rep4

description:
4818-EJ-4
fpkm_xol_l1
deseq2_xol1vsWT_l1.txt

source_name: WT control for xol-1 L1


title: act/inact3

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): TATCAGCCTA,GTTTCGTCCT,AGGACGAAAC
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C9


title: Fourth leaves,mutant, rep1

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the command "java -jar trimmomatic-0.38.jar PE $input1 $input2 $output1Paired $output1Unpaired $output2Paired $output2Unpaired ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads were mapped using HiC-Pro v 3.1.0 with the following setting "BOWTIE2_GLOBAL_OPTIONS = --very-sensitive -L 30 --score-min L,-0.6,-0.6 --end-to-end --reorder BOWTIE2_LOCAL_OPTIONS = --very-sensitive -L 20 --score-min L,-0.6,-0.6 --end-to-end --reorder GENOME_FRAGMENT = M82_v1.0_dpnii.bed" against the genome of M82_v1.0.
Assembly: M82 V1.0
Supplementary files format and content: allValidPairs files

extract_protocol:
Hi-C experiments were performed according to Concia et al (Concia et al, 2020) with modifications concerning a second crosslinking step, involving Disuccinimidyl Glutarate (DSG), and the use of a second restriction enzyme (DdeI) according to Lafontaine et al. (Lafontaine et al, 2021)
DNA libraries were then prepared using NEBNext Ultra II DNA library preparation kit (NEB) according to the manufacturer’s instructions (10 cycles for the PCR amplification step)


title: Lovo-WT3

first: Hanchen

address: No.725, South Wanping Rd

institute: Institute of Digestive, Longhua Hospital, Shanghai University of Traditional Chinese Medicine

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
he high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4).
edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis.
Genome_build: HG19
Supplementary_files_format_and_content: Matrix table with raw circRNA counts for every circRNA and every sample

source_name: colorectal cancer

growth_protocol: Human CRC cell lines (HCT116, Lovo) were purchased all purchased from the type Culture Collection of Chinese Academy of Sciences (Shanghai, China). HCT116 cells were cultured in DMEM (Gibco, Carlsbad, CA, USA), Lovo cells were cul-tured in F12 (Gibco, Beijing, China). All culture medium containing 10% fetal bovine serum and 1% penicillin and these cell lines were maintained in a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.

treatment_protocol: The HCT116, Lovo cells were exposed to an initial 5-Fu concentration of 0.1 μg/ml in medium plus 10% FBS. The surviving population of cells was grown to 80% confluence. 5-Fu resistant cells were established after sequential treatments of 5-Fu with increasing concentration of 5-Fu as 0.2, 0.5, 1, 1.5 and 2 μg/ml. Cells were able to survive at least 3 days of stimulation with a concentration of 5-Fu in 2 μg/ml. Resistance to 5-Fu was confirmed by WST-1 assay.

value: colorectal cancer

value: Lovo

tag: phenotype

value: sensitive (parental)


title: Lovo-5FuR1

value: 5-Fu resistant


title: WT_2, L1, rep3

description:
4818-EJ-3
fpkm_xol_l1
deseq2_xol1vsWT_l1.txt


title: act/inact2

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): ACGACTACCA,ACGACCCTAA,TTAGGGTCGT
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C6


title: WT_2, L1, rep2

description:
4818-EJ-2
fpkm_xol_l1
deseq2_xol1vsWT_l1.txt


title: act/inact5

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): AGAATGGTTT,GAGGGTGGGA,TCCCACCCTC
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C10


title: Fourth leaves,mutant, rep2


title: Lovo-WT2


title: CGM2

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): TGCGCGGTTT,CAAGGATAAA,TTTATCCTTG
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C1

value: non-demented control


title: Lovo-WT1


title: Fourth leaves,WT, rep1


title: Lovo-5FuR3


title: act/inact1

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): TCCGTTGGAT,ACGTTCTCGC,GCGAGAACGT
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C5


title: xol-1, early embryo, rep3

description:
3489-EJ-6
fpkm_xol1_ee
deseq2_xol1vsWT_ee.txt

source_name: xol-1 early embryo

value: early embryo


title: CGM1

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): TATTGAGGCA,CAGGTAAGTG,CACTTACCTG
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-B9

value: grey matter


title: CGM3

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): TCGGCTCTAC,CCGATGGTCT,AGACCATCGG
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-B5


title: Mutant fourth leaves,1-month-old,H3K9me2

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "java -jar trimmomatic-0.38.jar SE $input $output ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.5 with the following setting "bowtie2 --very-sensitive" against the genome of M82 V1.0 genome.
Filtering step: Mapped reads were filtered with samtools v.1.9 with the command "samtools view -h -b -q 30  "mapping_quality >= 30"
Duplicate filtering: duplicated reads were removed with samtools v.1.9 with the command "samtools fixmate -m  and samtools markdup -r "
Peak calling: peaks of read density were called with MACS3.0.0a6  with the command "macs3 callpeak --broad -t sample.bam -c Input.bam -g 829069930 -q 0.05  -B -n --outdir "
Bigwig generation: read density was scored with s3norm with the default paramaters
Assembly: M82 V1.0
Supplementary files format and content: bigWig, broadPeak


title: xol-1, L1, rep2

description:
4818-EJ-10
fpkm_xol_l1
deseq2_xol1vsWT_l1.txt


title: Lovo-5FuR2


title: xol-1, early embryo, rep2

description:
3489-EJ-5
fpkm_xol1_ee
deseq2_xol1vsWT_ee.txt


title: Mutant fourth leaves,1-month-old,H3K27me1


title: CWM2

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): GTGGATCAAA,GCCAACCCTG,CAGGGTTGGC
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-A2


title: HCT116-5FuR2


title: CWM1

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): GTAACATGCG,AGTGTTACCT,AGGTAACACT
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-A1


title: xol-1, early embryo, rep1

description:
3489-EJ-4
fpkm_xol1_ee
deseq2_xol1vsWT_ee.txt


title: HCT116-5FuR1


title: Mutant fourth leaves,1-month-old,H3K27me3,rep1


title: WT_2, L1, rep1

description:
4818-EJ-1
fpkm_xol_l1
deseq2_xol1vsWT_l1.txt


title: active4

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): GCAGTATAGG,TTCCGTGCAC,GTGCACGGAA
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-D4

value: multiple sclerosis


title: WT fourth leaves,1-month-old,H3K9me2


title: WT_1, early embryo, rep3

description:
3489-EJ-3
fpkm_xol1_ee
deseq2_xol1vsWT_ee.txt

source_name: WT control for xol-1 early embryo


title: active3

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): GCTACAAAGC,CACGTGCCCT,AGGGCACGTG
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C8


title: WT_1, early embryo, rep2

description:
3489-EJ-2
fpkm_xol1_ee
deseq2_xol1vsWT_ee.txt


title: WT fourth leaves,1-month-old,H3K27me1


title: WT_1, early embryo, rep1

description:
3489-EJ-1
fpkm_xol1_ee
deseq2_xol1vsWT_ee.txt


title: HCT116WT2


title: HCT116-5FuR3


title: active1

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): CACTACGAAA,TTAGACTGAT,ATCAGTCTAA
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-A3


title: active2

description:
sample index(i7), index2_workflow_a(i5), index2_workflow_b(i5): CGCGCACTTA,CCTGTATTCT,AGAATACAGG
dual indexing according to the Visium 10x kit (Dual Index Kit TT Set A (PN-1000215)), well SI-TT-C7


title: HCT116WT1


title: WT fourth leaves,1-month-old,H3K27me3


title: LAB_25_NP_rep10

status: Public on Aug 04 2024

city: Chapel Hill

first: Katherine

last: Malinski

address: 120 South Rd, Coker Hal #108

department: Biology

institute: University of North Carolina

data_processing:
Sequences were trimmed using cutadapt (v 4.1), assessed for quality control using FastQC (v 0.11.5), and aligned to both the M. sexta genome (GCF_014839805.1_JHU_Msex_v1.0, PMID: 33561252) and the circular CcBV genome (GCA_000844405.1_ViralMultiSegProj14556, PMID: 15472078). Uniquely mapped reads were counted via featureCounts read summarization software (v 2.0.4). An average of 36,317 reads per library aligned to the CcBV genome for parasitized (P) hosts, and 92 (presumably erroneously) for non-parasitized (NP) hosts. Parasitized host libraries with <300 reads aligning to the CcBV genome were assumed not successfully parasitized and were removed from the analysis (1 sample each from 25P and 40P lab population).
Assembly: Sequences were aligned to both the M. sexta genome (GCF_014839805.1_JHU_Msex_v1.0, PMID: 33561252) and the circular CcBV genome (GCA_000844405.1_ViralMultiSegProj14556, PMID: 15472078).
Supplementary files format and content: each matrix file is the output of FeatureCounts, and is in matrix format. One is from the M. sexta assembly (Ms_transcript_counts_matrix.mx), the other from the C. congregata bracovirus assembly (gffCcBV_counts_matrix.mx).

organism: Manduca sexta

source_name: fat body

growth_protocol: M. sexta were reared to the 3rd instar at 25C under 14L:10D conditions in environmental chambers, housed in individual petri dishes and fed an artificial lab diet supplemented with tobacco powder

extract_protocol:
RNA was extracted from fat body tissue of 8-10 M. sexta larvae per treatment group for each population using the Direct-zol RNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions, including a DNase I (Zymo Research) treatment step to remove genomic DNA from samples. RNA quality was assessed via Qubit 4 Fluorometer High Sensitivity RNA assay and NanoDrop Lite Plus Spectrophotometer (both Thermo Fisher Scientific).
RNA libraries were constructed via QuantSeq 3’ mRNA-Seq FWD Library Prep Kit for Illumina and purified via Purification Module with Magnetic Beads PCR Add-on Kit (both Lexogen) according to the manufacturer’s instructions. This method generates sequences from the 3’ end of mRNA transcripts, and has been demonstrated as an accurate and cost-effective alternative to whole mRNAseq methods. Library quality was assessed after the final PCR step via Qubit.

treatment_protocol: M. sexta larvae were parasitized by Cotesia congregata (P groups) or injected with an equivalent amount of Sephadex beads as a sham control (NP), or were unmanipulated (NOSHAM). Several hours later they were placed at either 25C or a heat shock of 40C for 24 hours. They were then removed and placed at 25C for an additional 24 hours prior to flash freezing for tissue extraction.

value: fat body

value: 3rd instar

value: University of North Carolina-Chapel Hill lab population

value: not parasitized by Cotesia congregata


title: LAB_25_NOSHAM_rep4

value: not parasitized by Cotesia congregata; not treated with sham control injection


title: LAB_25_NOSHAM_rep3


title: LAB_40_NOSHAM_rep2


title: LAB_40_NP_rep10


title: LAB_40_NOSHAM_rep3


title: LAB_40_NOSHAM_rep1


title: LAB_25_P_rep9

value: parasitized by Cotesia congregata


title: LAB_25_NOSHAM_rep2


title: LAB_25_NP_rep9


title: HCT116WT3


title: LAB_25_NP_rep8


title: LAB_25_P_rep8


title: LAB_40_NP_rep9


title: LAB_25_NP_rep7


title: LAB_40_P_rep9


title: LAB_25_NP_rep6


title: LAB_25_P_rep7


title: LAB_40_NP_rep7


title: LAB_25_P_rep6


title: LAB_40_P_rep8


title: LAB_40_P_rep7


title: LAB_40_P_rep6


title: LAB_40_NP_rep6


title: LAB_25_NOSHAM_rep1


title: LAB_25_P_rep5


title: LAB_25_NP_rep4


title: LAB_25_NP_rep5


title: LAB_25_P_rep3


title: LAB_40_P_rep3


title: LAB_25_P_rep4


title: LAB_40_NP_rep5


title: LAB_40_P_rep2


title: LAB_40_P_rep5


title: LAB_25_NP_rep2


title: LAB_25_NP_rep3


title: LAB_40_P_rep4


title: LAB_25_P_rep2


title: LAB_40_NP_rep1


title: LAB_40_P_rep1


title: LAB_40_NP_rep8


title: LAB_40_NP_rep2


title: LAB_25_P_rep1


title: FLD_40_P_rep10

value: North Carolina field population


title: FLD_40_NP_rep10


title: FLD_25_P_rep9


title: LAB_25_NP_rep1


title: FLD_25_NP_rep9


title: FLD_40_P_rep9


title: LAB_40_NP_rep4


title: FLD_40_NP_rep9


title: LABINFIELD_25_P_rep2


title: FLD_25_P_rep7


title: FLD_25_P_rep8


title: FLD_25_NP_rep8


title: FLD_25_NP_rep7


title: FLD_25_NP_rep6


title: FLD_40_P_rep8


title: FLD_25_P_rep6


title: FLD_25_NP_rep5


title: FLD_25_NP_rep4


title: FLD_40_P_rep7


title: LAB_40_NP_rep3


title: FLD_25_P_rep4


title: FLD_40_NP_rep8


title: FLD_25_NP_rep3


title: FLD_40_P_rep5


title: FLD_25_P_rep5


title: Funiculus, stk REP2

city: Porto

first: Sílvia

last: Coimbra

address: Rua do Campo Alegre s/n

country: Portugal

institute: LAQV/REQUIMTE, Faculty of Sciences, University of Porto

data_processing:
Illumina sequencing reads were generated using NextSeq 500 sequencer (Illumina).
Raw reads were cleaned and trimmed using Trimmomatic v.0.38 and were aligned against the Arabidopsis genome (Araport11) using STAR v.2.7.0 software with default parameters.
featureCounts v.1.6.3 was used to generate the count matrix and to calculate gene expression values as raw read counts.
Differentially expressed genes were identified using the DESeq2 package v.1.38.3 from R software v1.30.1.
Assembly: Araport11
Supplementary files format and content: Text file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: stage 17 Funiculus

growth_protocol: Arabidopsis thaliana wild-type (ecotype Columbia) and stk mutant plants were grown at 22°C under long-day conditions (16 h light/8 h dark).

extract_protocol:
mRNA was extracted from two biological replicates of 100 funiculi from stage 17 of both wt and stk, using the DynabeadsTM mRNA DIRECTTM Micro Kit (Invitrogen), according to the manufacturer’s instructions.
Sequencing libraries were prepared following the manufacturer’s instructions in the Low Sample protocol, using the TruSeq® RNA Sample Preparation v2 (Illumina Inc.).

value: stage 17 Funiculus

value: seedstick


title: FLD_40_NP_rep6


title: FLD_40_NP_rep3


title: Funiculus, stk REP1


title: Funiculus, wt REP2

value: wild-type


title: FLD_25_NP_rep2


title: FLD_40_P_rep4


title: Funiculus, wt REP1


title: FLD_25_P_rep3


title: NG_Treat 3

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. The RNA-seq data analyses were performed as previously described [64, 65]. Briefly, the FASTQ files were aligned to mouse mm10 genome using STAR 2.7.7a [66] with the following parameters: ‘–runThreadN 40 –outFilterMultimapNmax 1 –outFilterMismatchNmax 3 –outFilterScoreMinOverLread 0.25 –outFilterMatchNminOverLread 0.25’. A Perl script was used to calculate the total number of mapped reads and the number of reads that aligned to the exons of each gene. The table of raw read counts was normalized, and the top 1000 variable genes were selected to perform the principal component analysis by DESeq2 [67] and to perform the distance between variables by pheatmap. The edgeR [68] and the Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests (glmQLFTest) were used to compare the gene expression levels between the groups. The false discovery rate (FDR) < 0.05 was used as the cutoff to identify differentially expressed genes (DEGs). The functional enrichment analysis was performed using g:Profiler (version_e106_eg53_p16_65fcd97) and Gene set enrichment analysis (GSEA) software [69]. The list of DEGs were used as the input files for g:Profiler. Briefly, the Benjamini-Hochberg FDR with a threshold of 0.05 was used to determine the statistical significance and carried out to detect the Gene Ontology (GO), Reactome, and KEGG pathway. The gene ratio was defined as the intersection size divided by the query size. The intersection size, gene ratio, and adjusted P-value were used as input to generate a dot plot for GO enrichment analysis. The TPM values from edgeR were used as input files for the GSEA analysis. Briefly, the msigdb.v2022.1.Mm.symbols.gmt was used as gene sets database and Mouse-Gene_Symbol_Remapping_MsigDB.v2022.1.Mm.Chip was used as the chip platform. The parameters of ‘1000 permutation’, ‘collapse’ and ‘gene_set as permutation type’ were selected to run GSEA. The scripts used in this study are available at GitHub repository (https://github.com/Jerry-Zhao/NG2023).
Assembly: mm10
Supplementary files format and content: bigwig format files including the tracks for the data
Supplementary files format and content: tab-delimited text files include raw read count values for each sample

source_name: spinal cord

growth_protocol: Mice were housed in pathogen-free facilities and maintained on a 12-hour light/dark cycle in the Animal Care Facility at the Child Health Institute of New Jersey and New York Medical College. All studies and protocols were approved by the Rutgers University and New York Medical College Animal Care and Use Committees and were in accordance with the National Institutes of Health guidelines. All viral particles were produced at the Boston Children’s Hospital Viral Core and Vigene Biosciences. Blood glucose was monitored using an automated glucose monitor (Bayer) and plasma insulin was detected by ELISA (Crystal Chem). Animals were fasted overnight for 15 hours for glucose tolerance tests and glucose-stimulated insulin secretion assays and 6 hours for insulin tolerance tests.

extract_protocol:
RNA samples were quantified and assessed for quality using Agilent BioAnalyzer (Agilent Technologies, Palo Alto, CA, USA).  The RIN values were 7.95 +/- 0.86 [6.6 to 9.1] and a median concentration of 48.5 ng/ul but with a very wide range [1.8 to 266.6] ng/ul.
Illumina sequencing libraries were prepared using the Clontech/Takara Pico-Input Strand-Specific Total RNA-Seq for Illumina (Takara, San Jose, CA, USA) and barcodes for sequencing together as a pool. To compensate for the wide range of concentrations the same amount of RNA was used for each sample, roughly 6 ng of total RNA. The libraries were assessed for quality using a TapeStation (Agilent Technologies, Palo Alto, CA, USA) as well as the Kapa library quantification kit (KAPA Biosystems, Wilmington, MA, USA) The libraries had a median size of 407 +/- 13 bp. Samples were pooled in equimolar amounts and sequenced on an Illumina HiSeq 2000 in two separate lanes at 101 bp with 8x8bp barcodes.  FASTQ files were produced using Illumina bcl2fastq program with a read length of 100bp.

treatment_protocol: C57BL/6J male mice were anesthetized and infused, using osmotic pumps (ALZET) implanted subcutaneously, with PBS alone or PBS with the insulin receptor antagonist S961 at the dose of 10 nmoles/week for two weeks. For high-fat diet experiments, mice were challenged with a diet containing 60% kcal fat (catalog# D12492, Research Diet) for twenty-four weeks.

value: spinal cord

value: vagal jugular-nodose ganglia

value: jugular-nodose ganglia

value: WT


title: NG_Treat 2


title: LABINFIELD_40_P_rep2


title: LABINFIELD_40_NP_rep2


title: FLD_40_NP_rep7


title: NG_Ctrl 3


title: FLD_40_NP_rep5


title: LABINFIELD_25_NP_rep2


title: NG_Treat 1


title: FLD_40_P_rep6


title: FLD_40_NP_rep4


title: FLD_40_P_rep2


title: FLD_25_P_rep2


title: NG_Ctrl 1


title: FLD_25_P_rep10


title: dorsal forebrain organoids day 90

city: Shenzhen

first: honghui

last: zheng

state: Guangdong

address: Taoyuan Street

institute: Tsinghua University

description:
10X Genomics
Control forebrain organoids

data_processing:
ScRNA-seq libraries were integrated by Seurat (v5.0) under the R (v2.8.2) environment. The reads were aligned to the GRCh38 reference genome in Cellranger-7.0.0. We filtered high-quality cells based on the number of genes detected (min. 200, max 6000), genes expressed in cells (min. 10), gene-level unique molecular identifier (UMI) counts (min. 500), log10GenesPerUMI > 0.8 and removing cells with high mitochondrial (<20%) and ribosomal (<30%) mRNA content. Subsequently, the feature matrices were multiplied by 10,000 scaling factor and natural-log transformed. The top 2000 highly variable genes were then selected by Variance Stabilizing Transformation (VST) for downstream analysis. Principal component analysis (PCA) was performed on the expression matrices, and the top 25th PCs were used for downstream analysis. Cells were clustered in PCA space using Seurat’s FindNeighbors, followed by FindClusters with resolution = 2.0. Additionally, stressed cells were filtered out using the Gruffi R package before the removal of clusters expressing markers associated with unfolded protein response with manual inspection.
Following quality control, cells were clustered (FindClusters function; resolution = 0.2) and visualized with Uniform Manifold Approximation and Projection (UMAP). Cluster identities were assigned based on differentially expressed gene markers, top biological process annotations, correlation analysis with 6–22 gestational weeks (GW) primary brain ScRNA dataset (Bhaduri A et al. 2020) and literature. Differentially expressed genes (DEGs) for each cluster were identified via the FindAllMarkers function (log fold change threshold = 0.25). GO terms enrichment of each cluster was performed using the enrichGO function from the ClusterProfiler package (v.4.10.0). Enrichment was performed on biological process GO terms. Correlation analysis was generated similar to the previously reported48. Briefly, in the space of co-expressed marker genes, specificity, and enrichment scores were calculated using log2(fold change) of the marker and the percentage of cells expressing the marker compared to other clusters, accordingly. The final matrix of all markers across all clusters was created by multiplying the specificity and enrichment scores. The similarity of clusters between organoids and primary samples was correlated using Pearson’s correlations.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: organoid

growth_protocol: PSCs were maintained in MTESRTM Plus (STEMCELL Technologies, catalog # 100-0276) on Matrigel (Corning, catalog number 354277) coated plates and passaged once a week using Relesr (STEMCELL Technologies, catalog # 100-0483). Dorsal forebrain organoids were generated as previously described (Feng et al., 2023). In brief, 70%- 90% confluent cells were dissociated using accutase (Sigma-Aldrich, catalog number A6964) and plated into ultra-low-attachment 96 U-bottomed -well plates (Corning, catalog number 7007) in MTESRTM Plus medium supplemented with 50um Y27632 (MCE, catalogue number HY-10583) at density of 1500 cells per well for 2 days to generate embryoid body-like aggregates. From day 2 to 6, half of the medium was replaced with EB patterning medium. On days 6-9, half of the medium was replaced with a neural induction medium. On day 9, organoids were embedded in the induction medium and Matrigel (Corning, catalog number 354230) with 3:2 dilution for another 5 days. On day 14, embedded organoids were mechanically dissociated from Matrigel and transferred to an orbital shaker in 6 well plates supplementing with differentiation medium. From Day 35 to Day 70, Matrigel was added into the differentiation medium at 1% (v/v). At Day 70, the differentiation medium was replaced with a maturation medium.

extract_protocol:
5 organoids of each condition at day 90 were pooled together and washed three times with HBSS without Ca2+ and Mg2+ (STEMCELL Technologies, 37250). Single-cell suspensions were acquired via incubation with a papain-based dissociation (Miltenyi Biotec, 130-092-628). Prewarmed papain containing mix 1 (2 ml) was added to the organoids and incubated for 15-20 min at 37 °C with gentle agitation every 5 minutes. After triturating 5–10 times with 1,000 µl wide-bore, enzyme mix 2 was added and incubated for 10 minutes at 37 °C twice with P1000 and P200 pipette tips trituration steps. Cells were washed twice with PBS + 0.2% BSA and filtered through a 40 µm cell strainer. Viability and cell count were assessed using a Trypan Blue assay on the automated cell counter Countess (Thermo Fisher Scientific). Cells were centrifuged at 300g at 4℃ for 5mins and resuspended in ice-cold PBS + 0.2% BSA at a cell density of 1000 cells/μL.
Single-cell encapsulation and library preparation were performed according to the manufacturer’s protocol. Approximately 12,000 cells in each channel were loaded onto a Chromium Single Cell 3′ Chip (10× Genomics, PN-120236) and processed through a Chromium controller to generate single-cell gel beads in emulsions (GEMs) according to the manufacturer’s instructions. Captured libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit v.2 (10x Genomics, PN-120237) and sequenced on an Illumina Novaseq with a paired-end 150 bp (PE150) reading strategy.

treatment_protocol: For astrocyte-conditioned medium incubation, simply replacing the neurobasal medium with medium conditioned by mouse (CD1) cortex astrocytes in differentiation and maturation medium at day 14.

value: organoid

value: embryonic stem cell line H9

value: hESC-derived dorsal forebrain organoids  at day90

tag: age

value: Without astrocyte conditioned medium treated, using neurobasal medium


title: dorsal forebrain organoids day 90 with ACM treated

description:
10X Genomics
ACM treated forebrain organoids

value: hESC-derived dorsal forebrain organoids at day90

value: CD1 fetal mouse astrocyte conditioned medium treated


title: FLD_25_NP_rep1

value: fat body

value: 3rd instar

value: not parasitized by Cotesia congregata


title: IGROV1 Input

city: South San Francisco

first: Karen

last: Gascoigne

state: California

address: 1 DNA way

institute: Genentech

description: no antibody

data_processing:
Reads were aligned consecutively to the human genome (hg38) using the BWA algorithm (default settings). Duplicate reads were removed and only uniquely mapped reads used (mapping quality >= 25)
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Assembly: Hg38
Supplementary files format and content: BigWig

growth_protocol: RPMI, 10% heat-inactivated fetal bovine serum, 1% L-Glutamine, and 1% Pen/Strep

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 15 min and then quenched with 125 mM glycine for 5 min. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051).
Illumina sequencing libraries were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara).

treatment_protocol: where indicated 72h 1ug/ml doxycycline to induce CAS9 and PAX8 targeted gRNA expression

value: Ovarian cancer cell


title: IGROV1, minus dox, H3K27Ac ChIP

description: H3K27Ac antibody Active Motif cat# 39133, lot# 06921014


title: IGROV1, plus dox, SMARCA4 ChIP

description: SMARCA4/BRG1 antibody Abcam cat# ab110641, lot# GR3375498-10

value: 72h 1ug/ml doxycycline to induce CAS9 and PAX8 targeted gRNA expression


title: FLD_25_P_rep1

value: North Carolina field population

value: parasitized by Cotesia congregata


title: IGROV1, minus dox, SMARCA4 ChIP


title: FLD_25_NP_rep10


title: FLD_40_P_rep1


title: IGROV1, plus dox, PAX8 ChIP

description: PAX8 antibody Novus cat# NBP1-32440, lot# 42613


title: LABINFIELD_40_NP_rep1

value: University of North Carolina-Chapel Hill lab population


title: FLD_40_NP_rep2


title: LABINFIELD_40_P_rep1


title: IGROV1, minus dox, PAX8 ChIP


title: FLD_40_P_rep3


title: LABINFIELD_25_P_rep1


title: NG_Ctrl 2

value: spinal cord

value: vagal jugular-nodose ganglia


title: Sample_70

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
The raw short-read sequences  were preprocessed using the Rfastp R/Bioconductor package Rsubread package. The raw short-read sequences  were quality-checked and trimmed to remove adapters and low-quality bases using the Rfastp R/Bioconductor package.
The preprocessed reads were then aligned and mapped to the human genome reference GRCh38 using the Subread aligner algorithm provided by Rsubread R/Bioconductor package. The aligned reads (BAM files) from each sample were employed to calculate gene expression abundance at the whole-genome level using the featureCounts function provided by the Rsubread package.
For metatranscriptomic analysis, the obtained RNA sequencing data were processed using the Biobakery suite of tools: KneadData was used to separate the human and the non-human reads; taxonomic profiling was performed using MetaPhlAn to identify and quantify microbial taxa at species level present in the anal samples.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of the raw counts per sample
Supplementary files format and content: raw_counts.txt

source_name: ASCC

extract_protocol:
Total RNA was isolated from the collected samples using the miRNeasy Tissue/Cells Advanced Kits (Qiagen) following standard manufacturer's protocol. RNA concentration and integrity were measured on a Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA samples with RNA integrity number (RIN) over 7 were considered for RNA sequencing. The RNA samples were processed for directional RNA-seq library construction using the Illumina Total RNA Prep with Ribo-Zero Plus library preparation kit according to the manufacturer's protocol.
We performed  100 nt paired-end sequencing using an Illumina Novaseq 6000 platform and obtained ~80 million clusters per sample with 92% >Q30.

value: ASCC


title: LABINFIELD_25_NP_rep1


title: Sample_69


title: Sample_68


title: FLD_40_NP_rep1


title: Sample_66


title: Sample_67


title: Sample_65


title: HMC3 cells, rhPOSTN

city: Soochow

first: Hao

state: Jiangsu

address: 899 Pinghai Road

department: Department of Neurosurgery & Brain and Nerve Research Laboratory

institute: The First Affiliated Hospital of Soochow University

data_processing:
The mixed sequencing libraries of different samples were denatured with 0.1 M NaOH to generate single-stranded DNA, which was subsequently diluted to a concentration of 8 pM and amplified in situ via a reagent kit.
The ends of the generated fragments were sequenced for 150 cycles using a DNBSEQ-T7 sequencer.     The original sequencing data were subjected to quality control and comparison for statistical and quantitative analysis of gene and transcript expression.
Solexa pipeline version 1.8 (off-line base caller software, version 1.8) was adopted to perform image processing and base recognition.
FastOC software evaluates the sequencing quality of reads after removing adapters;     Genome version used in reads mapping is GenCode GRCh37.
The Ballgown R package was used to calculate expression differences between groups based on FPKM from genetic levels. Differentially expressed mRNAs (DEmRNAs) were determined by the Ballgown package under the conditions of fold change ≥1.5 and p value ≤ 0.05.
Assembly: hg37
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HMC3 cells

growth_protocol: The HMC3 cell line was cultured in MEM (including NEAA) supplemented with 10% FBS (VivaCell) and 1% PS. All cells were maintained at 37 ℃ and 5% CO2.

extract_protocol:
Total RNA was extracted and the concentration was measured by NanoDropND-1000. 1∼2 µg of total RNA was selected from each sample for RNA sequencing library construction.
1 ∼ 2 µg of total RNA was selected from each sample for sequencing library construction. Total RNA was first enriched for mRNA using NEB Next® Poly(A) mRNA Magnetic Isolation Module (or RiboZero Magnetic Gold Kit for rRNA removal). The processed RNA was used to construct the library using KAPA Stranded RNA-Seq Library Prep Kit (Roche).

treatment_protocol: HMC3 cells treated with PBS or human recombinant POSTN

value: HMC3 cells

value: microglia cells

value: WT

value: rhPOSTN


title: HMC3 cells, PBS

value: PBS


title: Fourth leaves,WT, rep2

value: 1-month-old leaves


title: Sample_63


title: DC2, p84KO, steady state, rep2

city: Paris

first: Despoina

last: Koumantou

address: 16 rue Henri Huchard

institute: INSERM U1149

data_processing:
FastQC using FastQC v0.11.9 tool
Adapter triming using TrimGalore v0.6.2 tool
Alignement on mm10 using STAR v 2.7.6a tool
Assembly: mm10
Supplementary files format and content: excel file includes raw counts for each sample

source_name: spleen

extract_protocol:
RNA was extracted using the Single Cell RNA purification kit (Norgen, Cat#51800) according to the manufacturer’s instructions with an additional DNAse treatment on-column
RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara).

value: spleen

value: type 2 conventional dendritic cells

value: p84 knockout

value: steady state


title: Sample_61


title: DC2, p84KO, steady state, rep3


title: Sample_62


title: Sample_60


title: DC2, p101KO, steady state, rep2

value: p101 knockout


title: DC2, p101KO, steady state, rep1


title: 141_WT_chl1sub1_N1

city: London

first: Thomas

middle: M.

last: Guerin

address: nw1 1at, 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Micro-C datasets were processed through the Distiller pipeline (https://github.com/open2c/distiller-nf, commit 8aa86e)
Reads were aligned to W303 using bwa 0.17.7 and the resulting maps filtered to remove low-quality alignments (MAPQ<30) and cis alignment pairs within 150 bp
Replicates were analysed independently, and their quality assessed before aggregation into sample-level datasets.
Merged contact matrix are provided in mcool files
Assembly: w303
Supplementary files format and content: mcool files contain the contact probabilities of merged replicates

organism: Saccharomyces cerevisiae

extract_protocol:
Micro-C was performed following published protocols[Costantino, 2020 #1788][Slobadyanyuk, 2022 #1888] with minor modifications. Yeast cultures were crosslinked with 3% formaldehyde for 15 minutes at 30 °C. The reactions were quenched by the addition of 250 mM glycine at 30 °C for 5 minutes with agitation. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 5 minutes and washed twice with water. Cells were then resuspended in Buffer Z (50 mM Tris-HCl pH 7.5, 1M sorbitol, 10 mM β-mercaptoethanol) and spheroplasted by addition of 250 mg/ml Zymolyase (100T) in a 30 °C incubator at 200 rpm for 40 to 60 minutes. Spheroplasts were washed once by 4 °C PBS and then pelleted at 4000 rpm at 4 °C for 10 minutes. Chromatin was further crosslinked by suspending pellets in PBS supplemented with 3 mM disuccinimidyl glutarate (ThermoFisher) and incubated at 30 °C for 40 minutes with gentle shaking before quenching by addition of 400 mM glycine for 5 minutes at 30 °C. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 10 minutes, washed once with ice-cold PBS and stored at −80 °C. Pellets were then treated as described[Costantino, 2020 #1788] until the de-crosslinking step. The De-crosslinking solution was added with an equal volume of phenol-chloroform-isoamyl alcohol (25:24:1), vortexed intensively and centrifuged for 15 minutes at room temperature. The aqueous phase was purified on a ZymoClean column (Zymo Research) according to the manufacturer instructions. Dinucleosome-sized DNA fragments were purified and excised from a 3% NuSieve GTG agarose gel (Lonza) using the Zymoclean Gel DNA Recovery Kit (Zymo).
17 ul of recovered DNA were treated with an end polishing following End-It DNA End-Repair Kit (Lucigen) manufacturer instruction before being diluted in 125 μL of water and added with 150 μL of 2x BW buffer. Biotynilated DNAs were precipitated using 5 μL of Dynabeads™ MyOne™ Streptavidin C1 for 30 minutes at 25 °C on a nutator. Beads were washed twice in 1x TBW buffer at 55 °C and once in 10 mM Tris HCl pH 7.5. Beads were then treated following NEBNext® Ultra™ DNA Library Prep Kit for Illumina® procedure. Briefly, beads were resuspended in 30 μL of End prep master mix and incubated according to the manufacturer instruction, followed by a standard adaptator ligation and USER enzyme digestion protocol. Adaptors were then washed 2 times in 1x TBW at 55 °C followed by one wash in 10 mM Tris pH 7.5. Beads were resuspended in 20 μL of Zymo Elution Buffer and an on-bead PCR was performed (8 to 12 cycles). Two rounds of 0.85X AMPure cleanup were performed. DNA fragments size were assessed on a Tapestation. Library were sequenced using an Illumina NovaSeq 6000 sequencer (100 bp paired). (see Slobodyanyuk et al. 2022 https://doi.org/10.1007/978-1-0716-2497-5_4)
micro-c

value: MATa


title: Sample_59


title: 6901_top2-4_top1_topA_N3

value: MATa/a top2-4 top1-delta::KlTRP1p pGPD-TopA::LEU2


title: 6901_top2-4_top1_topA_N2


title: 6901_top2-4_top1_topA_N1


title: Sample_58


title: 6900_top2-4_top1_N2

value: MATa/a top2-4 top1-delta::KlTRP1


title: Sample_57


title: DC2, WT, steady state, rep2


title: 6900_top2-4_top1_N3


title: 6900_top2-4_top1_N1


title: Sample_64


title: Sample_56


title: Sample_55


title: 6891_Scc3-AID_Treated_N2

value: MATa pADH1-OsTIR1-myc9::ADE2 HIS3::pMET3 -scc3-aid ::KlLEU2


title: DC2, p84KO, steady state, rep1


title: DC2, WT, steady state, rep1


title: 6891_Scc3-AID_Treated_N1


title: 6885_Scc3-AID_Untreated_N2

value: MATa pADH1-OsTIR1-myc9::ADE2 scc3-aid ::KlLEU2


title: 6863_sub1_N1

value: MATa sub1-delta::KlTRP1


title: Sample_54

value: ASCC


title: DC2, p101KO, steady state, rep3


title: 6875_chl1_G1_N1

value: MATa pGAL1-10- SICV5,V33 A76::ADE2 chl1 -delta::KlTRP1


title: DC1, WT, steady state, rep2

value: type 1 conventional dendritic cells

value: WT


title: DC2, WT, steady state, rep3


title: DC1, WT, steady state, rep1


title: 6885_Scc3-AID_Untreated_N1


title: Sample_52

source_name: HGSIL

value: HGSIL


title: 6750_WT_G1_N1

value: MATa pGAL1-10-Sic1 SIC1V5,V33 A76::TRP1


title: TG75_G2Depleted_35_N2

extract_protocol:
Micro-C was performed following published protocols[Costantino, 2020 #1788][Slobadyanyuk, 2022 #1888] with minor modifications. Yeast cultures were crosslinked with 3% formaldehyde for 15 minutes at 30 °C. The reactions were quenched by the addition of 250 mM glycine at 30 °C for 5 minutes with agitation. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 5 minutes and washed twice with water. Cells were then resuspended in Buffer Z (50 mM Tris-HCl pH 7.5, 1M sorbitol, 10 mM β-mercaptoethanol) and spheroplasted by addition of 250 mg/ml Zymolyase (100T) in a 30 °C incubator at 200 rpm for 40 to 60 minutes. Spheroplasts were washed once by 4 °C PBS and then pelleted at 4000 rpm at 4 °C for 10 minutes. Chromatin was further crosslinked by suspending pellets in PBS supplemented with 3 mM disuccinimidyl glutarate (ThermoFisher) and incubated at 30 °C for 40 minutes with gentle shaking before quenching by addition of 400 mM glycine for 5 minutes at 30 °C. Cells were pelleted by centrifugation at 4000 rpm at 4 °C for 10 minutes, washed once with ice-cold PBS and stored at −80 °C. Pellets were then treated as described[Costantino, 2020 #1788] until the de-crosslinking step. The De-crosslinking solution was added with an equal volume of phenol-chloroform-isoamyl alcohol (25:24:1), vortexed intensively and centrifuged for 15 minutes at room temperature. The aqueous phase was purified on a ZymoClean column (Zymo Research) according to the manufacturer instructions. Dinucleosome-sized DNA fragments were purified and excised from a 3% NuSieve GTG agarose gel (Lonza) using the Zymoclean Gel DNA Recovery Kit (Zymo).
17 ul of recovered DNA were treated with an end polishing following End-It DNA End-Repair Kit (Lucigen) manufacturer instruction before being diluted in 125 μL of water and added with 150 μL of 2x BW buffer. Biotynilated DNAs were precipitated using 5 μL of Dynabeads™ MyOne™ Streptavidin C1 for 30 minutes at 25 °C on a nutator. Beads were washed twice in 1x TBW buffer at 55 °C and once in 10 mM Tris HCl pH 7.5. Beads were then treated following NEBNext® Ultra™ DNA Library Prep Kit for Illumina® procedure. Briefly, beads were resuspended in 30 μL of End prep master mix and incubated according to the manufacturer instruction, followed by a standard adaptator ligation and USER enzyme digestion protocol. Adaptors were then washed 2 times in 1x TBW at 55 °C followed by one wash in 10 mM Tris pH 7.5. Beads were resuspended in 20 μL of Zymo Elution Buffer and an on-bead PCR was performed (8 to 12 cycles). Two rounds of 0.85X AMPure cleanup were performed. DNA fragments size were assessed on a Tapestation. Library were sequenced using an Illumina NovaSeq 6000 sequencer (100 bp paired). (see Slobodyanyuk et al. 2022 https://doi.org/10.1007/978-1-0716-2497-5_4)

value: MATa URA3::pMET3-scc2-aid::KANMX6 pADH1-OsTIR1-MYC9::ADE2 SMC3-PK3::HIS3MX rat1-1::LEU2


title: 6750_WT_G1_N2


title: TG75_G2Depleted_35_N1


title: Sample_51


title: L.N UV2

city: Tel Aviv

first: Carmit

last: Levy

state: israel

address: kalchekin 35

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

data_processing:
FASTQ files were created using CellRanger mkfastq function (v7 10×Genomics)63. Gene counts were obtained by aligning reads to the mm10 genome using CellRanger count function. To remove doublets and poor-quality cells, we excluded cells that: Contained more than 25% mitochondrially-derived transcripts. Contained less than 200 or more than 5,000 genes detected. Contained less than 200 or more than 25,000 detected molecules. The filtering process yielded 33,703 cells. Four samples of lymph nodes from control mice and 3 samples of lymph nodes of UV treated mice were merged and transcript counts were normalized and scaled using the NormalizeData ScaleData functions in Seurat 4.3.264 R package, which normalizes scales, and centers features in the dataset. For principal component analysis (PCA) and clustering, we used a log-transformed expression matrix. Variably expressed genes were used to construct principal components (PCs) and PCs covering the highest variance in the dataset were selected. The selection of these PCs was based on an elbow plot.
Clusters were calculated by the FindClusters function with a resolution between 0.25 and 0.35 and visualized using the t-SNE dimensionality reduction method. The FindClusters function in Seurat was used to identify clusters of cells by a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm. First, we calculated the k-nearest neighbors and constructed the SNN graph. To generate tSNE plots of single cell profiles, we used the Seurat's RunTSNE function
Single-cell gene signature scoring was done as described previously65. Briefly, as an initial step, to remove bias towards highly expressed genes the data was scaled using z-score across each gene. For a given gene signature (list of genes), a cell-specific signature score was computed. Scores were computed by first sorting the normalized scaled gene expression values for each cell followed by summing up the indices (ranks) of the signature genes. The same method was also applied to gene-signatures which includes both up-regulated and down-regulated genes. In this case, two ranking scores were obtained separately, and the down-regulated associated signature score was subtracted from the up-regulated generated signature score. A contour plot which takes into account only those cells that have a signature score above the indicated threshold was added on top of the tSNE space, in order to further emphasize the region of highly scored cells.
Assembly: FASTQ files were created using CellRanger mkfastq function (v7 10×Genomics)63.

source_name: Lymph nodes

growth_protocol: Spleen and lymph node were homogenized in Hank’s balanced salt solution (Gibco) supplemented with 2% FBS and 5 mmol/L EDTA and were isolated through a 70-μm strainer (Corning). Tumors were digested in RPMI 1640 with 2 mg/mL collagenase IV, 2,000 U/mL DNase I (Sigma Aldrich) for 30 minutes at 37 °C and then homogenized and strained through a 70-μm strainer.

extract_protocol:
. Lymph nodes and liver were homogenized, and total RNA was extracted using Trizol (Invitrogen). cDNA was produced using the cDNA SuperMix kit (QuantaBio) and then subjected to qRT-PCR using the Blue SYBR low ROX kit (PCR Biosystems). mRNA levels were normalized to endogenous actinβ. Naïve lymph nodes and liver were used as negative controls. The qRT-PCR primers were mCherry forward, 5'-GAACGGCCACGAGTTCGAGA-3'; mCherry reverse, 5'-CTTGGAGCCGTACATGAACTGAGG-3'; actinβ forward, 5'-CTGTCCCTGTATGCCTCTG-3'; and actinβ reverse, 5'-ATGTCACGCACGATTTCC-3'. For the other genes we used these primers:  36B4 forward, 5'-GATGATCAAAGGGATGTGGC-3' and reverse, 5'-AGCTCGGCAACAGACTCTTC-3'.
10μL of sorted cells were stained with Trypan Blue and counted using a hemocytometer and optical microscope. Cells were then centrifuged at 300 G for 5 min, resuspended into sorting medium at concentration of 1000 cells/ μL. Cells were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 30 Reagent Kits v3 according to manufacturer’s protocol (10× Genomics). The generated single-cell RNA-seq libraries were sequenced using a 75 cycle NextSeq 500 high output V2 kit.

treatment_protocol: For killing assays, mononuclear layers were collected from splenocyte suspensions using Ficol Histopaque®-1077 (Sigma Aldrich), washed by adding 10 mL of RPMI 1640 medium, and centrifuged at 700 xg for 10 minutes at 18 °C. The pellet of spleen mononuclear cells or the pellet of sDLN cells was re-suspended in MACS buffer (0.5% BSA, 2 mM EDTA in PBS). CD8+ T-cells enrichment was conducted using CD8 mouse magnetic MicroBeads (Miltenyi Biotec) according to manufacturer's instructions. CD4+ and CD8+ cells were enriched by negative selection using Pan T-cells Isolation Kit II, mouse (Miltenyi Biotec). CD11b+cells were isolated using magnetic CD11b MicroBeads and column (both from Miltenyi Biotec). Ly6anegative/low T-cells were sorted from spleen mononuclear cells using FACS (BD FACSAria III, BD Biosciences).

value: Lymph nodes

value: not relevant

value: UVB


title: L.N UV3