title: Stimulated microglia - pcHi-C_rep2

data_processing:
All reads were quality trimmed using fastp.
Reads were mapped, filtered, and deduplicated using HiCUP 0.7.1 running bowtie2 and retaining ditags with lengths between 100 and 1200 bp.
Paired-end BAM files from HiCUP were converted to CHiCAGO input format and interactions were called using CHiCAGO with minNPerBaits=250 and a score cutoff of 5.
Assembly: hg19
Supplementary files format and content: CHiCAGO interaction data in IBED format

growth_protocol: Microglia differentiation is started from human iPSC. Once the clones becomes apparent, the differentiation is induced in chemically defined commercial medium by transient, stage specific exposure of growth factors, including BMP4, FGF2, VEGF-A, SCF, TOP, IL-3, Flt3, M-CSF and GM-CSF. Microglia like precursors co-expressing CD14, CD45 and CX3CR1 are detached from adherent hemotopoigetic progenitors and are seeded in medium containing GM-CSF and IL-34 for mature differentiation lasting 2 weeks.

extract_protocol:
Cells were harvested, fixed in 1% formaldehyde, snap frozen in dry ice, then stored at -80C. Nuclei extraction was performed prior to further processing.
In situ Hi-C was performed using the standard protocol, then 500 ng of the resulting libraries were used to prepare pcHi-C using a custom biotinylated RNA probe set. In
In situ Hi-C followed by pcHi-C

treatment_protocol: iPSC-microglia are incubated with IFN-beta (100U/ml, R&D, Cat 8499-IF) for 6hr.

value: Microglia


title: Trim33KO_HU

status: Public on Jul 28 2023

type: SRA

city: Tübingen

first: Nikita

last: Popov

address: Otfried-Müller-Str 14

department: Clinical Tumor Biology

country: Germany

institute: University Hospital Tübingen

library_source: genomic

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to mouse genome (mm9) with STAR (version 2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
Sequencing tag coverage was calculated using Homer annotatePeaks script
Assembly: mm9
Supplementary files format and content: Bedgraph

molecule: genomic DNA

organism: Mus musculus

source_name: liver

growth_protocol: p19Nras cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Pen-Strep in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The assay was performed as described previously (Lensing et al, 2016) with modifications. Cells were fixed with formaldehyde and permeabilized with 0.2% Triton X-100 in PBS. DNA end repair reaction was performed by incubation with E.Coli DNA Polymerase I Klenow fragment for 30 minutes at 25C. Cells were washed and A-tailing reaction was performed in dA-tailing buffer (NEB) with Klenow exo- for 30 minutes at 37C. dA-tailed DNA fragments were ligated to a biotinylated NEB adapter at 16C overnight. Cells were lysed in 20mM Tris pH8.5, 300mM NaCl, 0.2%SDS and treated with proteinase K, followed by sonication, phenol-chloroform extraction and ethanol purification of DNA. Biotinylated DNA fragments were captured on Streptavidin beads and used for library preparation with NEB Ultra II DNA library end prep kit.
Sequencing libraries were prepared using NEB Ultra II DNA library Prep kit according to the manufacturer’s instructions.
DSB capture and sequencing

treatment_protocol: Hydroxyurea at 1mM for 24 hours with or without subsequent release for 24 hours

tag: tissue

value: liver

tag: cell line

tag: cell type

value: HCC

tag: genotype

tag: treatment

value: HU


title: Trim33WT_HU

value: sgCtrl


title: Hi-C siRad21 replicate3

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

data_processing:
Sequenced paired-end 150-bp reads were mapped to the human genome hg38 using Juicer version 1.5.7 (BWA 0.7.12-r1039) with default parameters.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: The hic files were generated by juicertools version 1.9.9 with default parameters. We used "inter_30.hic" in which low-quality reads were filtered.

organism: Homo sapiens

source_name: RPE cells

growth_protocol: RPE cells were routinely cultured in DMEM supplemented with penicilline-streptomycin-L-glutamine solution (Wako) and 10% FBS.

extract_protocol:
Hi-C experiments were performed using MboI restriction enzyme as previously described (Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680, doi:10.1016/j.cell.2014.11.021 (2014)).  Briefly, RPE cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Cells were permeabilized and chromatin was digested with MboI restriction enzyme, and the ends of restriction fragments were labeled with biotinylated nucleotides and ligated.  After crosslink reversal, DNA was purified and sheared with Covaris M220 (Covaris).  Then point ligation junctions were pulled down with streptavidin beads.
Sequencing libraries were constructed using Nextera Mate Pair Sample Preparation Kit (Illumina) according to the manufacturer’s protocol with 15 PCR cycles.

treatment_protocol: RNAi transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in accordance with the manufacturer's protocol, using final RNA duplex concentration of 50 nM.

tag: enzyme

value: MboI

value: Rad21 siRNA

tag: time point


title: HepG2 cells_rep1-0 min after insulin stimulation

city: Cambridge

first: Charalampos

last: Lazaris

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute for Biomedical Research

library_source: transcriptomic

data_processing:
RNA-seq reads were processed using nf-core RNA-seq pipeline v1.4.2 (single-end with strandedness set to reverse). Low-quality reads were trimmed using Trim Galore! v0.6.4. Alignment was performed using STAR v2.6.1d. Transcript quantification was perform using featureCounts v1.6.4. StringTie was used to calculate FPKM.
ChIP-seq reads were processed using the nf-core ChIP-seq pipeline v1.2.1. Trim Galore! v0.6.4_dev was used to trim low-quality reads. Alignment was performed against the hg19 genome assembly using BWA v0.7.17-r1188. Peak calling was performed using MACS2 v2.2.7.1 and peak annotation using Homer.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files either contain gene expression values or raw count values for the RNA-seq data. For ChIP-seq data, we provide .bigwig files for genome brower visualization. ChIP-seq peaks were called with MACS2 and annotated with Homer

molecule: total RNA

source_name: HepG2 cell line

growth_protocol: EMEM 10% FBS

extract_protocol:
DNA extraction
NEBNext UltraTM II kit
75-bp single-end reads

treatment_protocol: EMEM for 16hrs, EMEM BSA and 3nM insulin for 5min

value: liver hepatocellular carcinoma


title: Stimulated microglia - pcHi-C_rep1

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

source_name: WTC11 iPSC-derived Microglia

value: WTC11 iPSC-derived Microglia


title: Trim33KO_Ctrl

value: Vehicle (water)


title: HepG2 cells_rep2-0 min after insulin stimulation


title: Resting microglia - pcHi-C_rep2

treatment_protocol: No IFN-beta stimulation.


title: HepG2 cells-INSR_input

extract_protocol:
Tryzol
KAPA HyperPrep stranded RNA
50 bases, single-end reads

treatment_protocol: EMEM per 2 days, EMEM 0.1% insulin and BSA for 2 days, washout for 30min and stimulation with 3nM insulin in EMEM BSA

tag: chip antibody

value: Dynabeads Protein A/G


title: Trim33WT_Ctrl


title: Hi-C siPDS5B

value: PDS5B siRNA


title: H1-derived microglia (stimulated) - ATAC_rep2

description:
H1_stim_idr_optimal_peak.narrowPeak
h1MG_atac_stim.bw

data_processing:
All libaries were processed using the ENCODE ATAC-seq pipeline (v1.8.0) using default settings
Briefly, reads were mapped to bowtie2, duplicates removed by picard and peaks were called by MACS2
Assembly: hg19
Supplementary files format and content: Optimal IDR peak called using MACS2
Supplementary files format and content: bigwig file was generated with bamCoverage --binSize=1 and merged with UCSC bigWigMerge

source_name: H1 ESC-derived Microglia

growth_protocol: Microglia differentiation is started from human hESC H1. Once the clones becomes apparent, the differentiation is induced in chemically defined commercial medium by transient, stage specific exposure of growth factors, including BMP4, FGF2, VEGF-A, SCF, TOP, IL-3, Flt3, M-CSF and GM-CSF. Microglia like precursors co-expressing CD14, CD45 and CX3CR1 are detached from adherent hemotopoigetic progenitors and are seeded in medium containing GM-CSF and IL-34 for mature differentiation lasting 2 weeks.

extract_protocol:
Cells were harvested, washed with ice cold PBS containing protease inhibitor and nuclei were extracted prior to library construction.
The standard ATAC-seq protocol was used, with the transposase reaction carried out for 30 minutes at 37C. 8-10 cycles of amplification were performed and dual size selection was performed with SPRIselect beads.

treatment_protocol: H1-microglia are incubated with IFN-beta (100U/ml, R&D, Cat 8499-IF) for 6hr.

tag: group

value: stimulated

value: H1 ESC-derived Microglia


title: Hi-C siPDS5A 48h

value: PDS5A siRNA


title: HepG2 cells-INSR_rep1

value: Insulin Receptor Antibody (IR) (Bethyl A303-712A)


title: Resting microglia - pcHi-C_rep1


title: Trim33WT_HA_Recql_HU_HA

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to mouse genome (mm9) with STAR (version 2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
Sequencing tag coverage was calculated using Homer annotatePeaks script
Assembly: mm9
Supplementary files format and content: Bedgraph
Library strategy: Cut&Run

extract_protocol:
Cells were fixed with 0.2% formaldehyde and Cut&Run assay was performed using the  mouse HA antibodies (#2367S) and the NEB CUT&RUN kit (#86652P)
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's protocol

treatment_protocol: Hydrohyurea at 1 mM (or vehicle - water) was added to cell culture medium for 4 hours

tag: antibody

value: anti-HA


title: microglia CRISPRi-hypr-seq screen rep1

description:
targeted single cell RNA-seq library
probes_hyprseq.tsv

data_processing:
Filter reads with fastp
Extract cell barcodes with UMI-Tools
Map reads to custom index with Bowtie
Convert to bam files with SAMTools
Generate count tables with UMI-Tools
Assembly: hg19
Supplementary files format and content: count tables (cells by probes or cells by genes) for all cells that passed QC
Library strategy: HyPR-seq

molecule: cytoplasmic RNA

extract_protocol:
The HyPRseq experiment was performed according to the published protocol (33376219). Briefly, cells were fixed in 4% formaldehyde solution and permeabilized in 70% ice cold ethanol. 4 pairs of ssDNA probes for each target gene were designed using HyPR-seq pipeline (https://github.com/EngreitzLab/hypr-seq). All probes were pooled at 20nM and incubated overnight at 37. After hybridization cells were washed and sequentially incubated with B1H1 hairpin (HCR tech), readout oligo, T4 ligase at 37°C for one hour individually. Following ligation, cells were resuspended in PBST and filtered through a 20 μm pluriStrainer. Single cell suspension was checked under microscope and counted for droplet generation.
To generate emulsions we first combined 1× EvaGreen Supermix (Bio-Rad Cat #186- 4033), 500 nM indexing primer, 2,000 cells and 20,000 barcoded beads (Chemgenes, as described above) in a 20 μLreaction. Once the PCR mix is made, emulsions were generated using QX200 Digital Droplet Generator (Bio-Rad #1864002) as per manufacturer’s instructions. After the droplets were generated, emulsions were gently transferred into PCR tubes and placed on ice and under the UV lamp (6.5 J/cm2 at 365 nm) about 3-8 cm away from the bulb for 5 mins. After UV exposure, the following cycling conditions were used for droplet PCR amplification: denaturation: 94°C for 30 sec; cycling: 25 cycles of 94°C for 5 sec, 64°C for 30 sec, and 72°C for 30 sec; final extension: 72°C for 5 mins. All PCR cycling steps were performed with 50% ramp rate (2 °C/min).To break down emulsions, PCR product were combined and half volume of 97% 1H,1H,2H,2H-Perfluoro-1-octanol (Sigma-Aldrich #370533) was added. Then tubes were vortexed for 5 sec and spun at 1000 g for 1 min. The top aqueous layer was carefully removed and cleaned with 1.8X SPRI beads according to manufacturer’s instructions. The amplicon libraries were sequenced with customer primers in deep sequencing. For each replicate we loaded ~50k cells in the emulsion generation step and ~15k cells could be packaged into droplets according to the Poisson distribution. We sequenced ~5000 reads/cell covering 18 target genes and 28 gRNA barcode sequences.


title: N2 (WT), adult day 2, replicate 2

city: Rochester

first: Andrew

middle: V

last: Samuelson

state: NY

address: 601 Elmwood Ave

department: Biomedical Genetics

institute: University of Rochester Medical Center

data_processing:
Raw FASTQ files were quality-checked with FastQC (Andrews 2010), and then trimmed to remove low-quality content and reads with Trimmomatic (Bolger at al 2014). An average of 30 million reads per sample remained after trimming.
RNA-Seq reads were aligned to the C. elegans genome (assembly WBcel235) with STAR 2.4.2a (Dobin et al 2013), using gene annotation from Ensembl (version 82). An average of 90.2% of reads per sample were uniquely and unambiguously mapped to the genome.
Gene-level counts were produced with featureCounts (SubRead package, version 1.4.6-p5), with exclusion of ambiguous or multi-mapping reads. Transcript quantification to obtain TPM (Transcripts Per Million) expression estimates were obtained with RSEM (Li and Dewey, 2011).
Counts and TPM matrices were filtered to remove genes with fewer than 10 counts in any sample, and were also filtered to keep only genes of specific biotypes based on Ensembl annotation: "lincRNA", "protein_coding", "ncRNA", "pseudogene", "snRNA", "antisense", as we expect that only poly-adenylated transcripts were included in the sequenced libraries. Exploratory analysis was performed with TPM expression values, or VST (Variance Stabilizing Transformation)-normalized counts as implemented in DESeq2 (Love et al, 2014).
Assembly: C elegans WS253
Supplementary files format and content: Raw counts from FeatureCounts (Liao et al. Bioinformatics 30.7 (2014): 923-930.), filtered for genes with evidence of expression (counts ≥ 10 in at least one sample), and for genes with expected poly-adenylation. 16828 genes in total passed the filter criteria.
Supplementary files format and content: TPM (Transcripts Per Million) filtered for genes with evidence of expression (based on raw counts ≥ 10 in at least one sample), and for genes with expected poly-adenylation. 16828 genes in total passed the filter criteria. TPM calculated with RSEM (Li, Bo, and Colin N. Dewey. BMC bioinformatics 12.1 (2011): 1-16.)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Each animal strain was grown on separate 10 cm RNAi agar plates, with 1 mL 10x concentrated HT115 bacteria on each plate. Animals were kept at 20°c on OP50 bacteria prior to preparation for the experiment. N2 or hpk-1(pk1393) animals were synchronized by bleach prep followed by synchronization at the L1 stage by overnight incubation in M9 to allow hatching. Approximately 1000 animals were added to a plate, with multiple plates for a given condition to reach approximately 3000 total animals each. Plates were kept at 16 °C during development, from L1 to L4. At the L4 stage, 600 µL of 4 mg/mL 5-fluorodeoxyuridine (FUdR) was added to prevent production of progeny, and animals were transferred to 20 °C. Each biological replicate sample was derived from a separate "egg prep".

extract_protocol:
When animals reached day 2 of adulthood, they were washed off and collected from the plates in M9 buffer, followed by two washes in M9, and a final wash with DEPC-treated RNase-free water.  Approximately two times the volume of the animal pellet of TRIzol® reagent was added to each animal preparation, followed by brief mixing and freezing overnight at -80 °C. Tubes were then allowed to partially thaw, and were vortexed for five minutes to assist with disrupting the cuticle. Each sample was transferred to a new tube, and 200 µL of chloroform per 1 mL of TRIzol was added to each tube, followed by vortexing for 20 seconds, and the tubes were allowed to settle at room temperature for 10 minutes. The supernatants were transferred to new tubes, and an equal amount of 100% ethanol was added and mixed before proceeding to column purification with the Qiagen RNAeasy Mini kit according the manufacturer’s instructions. Samples were eluted with 30 – 50 µL of DEPC-treated water, and checked for initial concentration and quality with a Nanodrop ND-1000 spectrophotometer.
Isolated RNA was provided to the University of Rochester Genomics Research Center for library preparation and sequencing. Prior to library preparation, RNA integrity of all samples was confirmed on an Agilent 2100 Bioanalyzer. Libraries for sequencing were prepared with the Illumina TruSeq Stranded mRNA kit, according to the manufacturer’s instructions. Quality of the resulting libraries was checked again with a Bioanalyzer prior to sequencing to ensure integrity.

tag: age

value: Adult D2

tag: sample type

value: whole animal, hermaphrodites

tag: food source

value: HT115 E. coli, expressing L4440 (Empty vector for RNAi feeding)

tag: temperature

value: whole organism


title: Trim33KO_HA_Recql_Ctrl_HA

value: liver

value: HCC

value: Vehicle


title: N2 (WT), adult day 2, replicate 3


title: Hi-C siRad21 siNIPBL double

value: MboI

value: Rad21siRNA & NIPBL siRNA#1


title: Hi-C siPDS5A siPDS5B double

value: PDS5A siRNA & PDS5B siRNA


title: Hi-C siRad21 replicate2

value: Rad21 siRNA


title: Hi-C siRad21 replicate1


title: Hi-C siNIPBL si8

value: NIPBL siRNA#2


title: Trim33WT_HA_Recql_Ctrl_HA

value: sgCtrl


title: hpk-1(pk1393), adult day 2, replicate 3


title: Trim33KO_HA_Recql_HU_input

value: HU


title: H1-derived microglia (stimulated) - ATAC_rep1

value: Microglia

value: stimulated

value: H1 ESC-derived Microglia


title: hpk-1(pk1393), adult day 2, replicate 2

value: Adult D2


title: WTC11-derived microglia (stimulated) - ATAC_rep2

description:
WTC11_stim_idr_optimal_peak.narrowPeak
wtcMG_atac_stim.bw

value: WTC11 iPSC-derived Microglia


title: Hi-C siNIPBL 72h

value: NIPBL siRNA#1


title: Trim33WT_HA_Recql_HU_input


title: Hi-C siPDS5A 72h

value: PDS5A siRNA


title: H1-derived microglia (resting) - ATAC_rep1

description:
H1_rest_idr_optimal_peak.narrowPeak
h1MG_atac_rest.bw

value: resting


title: Hi-C siNIPBL 48h


title: hpk-1(pk1393), adult day 2, replicate 1

value: whole animal, hermaphrodites

value: HT115 E. coli, expressing L4440 (Empty vector for RNAi feeding)

value: whole organism


title: Hi-C siNIPBL 24h

value: MboI


title: WTC11-derived microglia (resting) - ATAC_rep2

description:
WTC11_rest_idr_optimal_peak.narrowPeak
wtcMG_atac_rest.bw


title: H1-derived microglia (resting) - ATAC_rep2


title: Trim33WT_HA_Recql_Ctrl_input

value: liver

value: HCC

value: Vehicle


title: N2 (WT), adult day 2, replicate 1


title: cDC2_Cd47DT_3

city: Kobe

first: Yasuyuki

last: Saito

state: Hyogo

address: 7-5-1, Kusunoki-cho, Chuo-ku

department: Biochemistry and Molecular Biology, Division of Molecular and Cellular Signaling

institute: Kobe University Graduate School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse reference genome (GRCm38) with the STAR aligner.
Raw read counts were obtained with RSEM and were normalized for further analysis with the use of the built-in normalization algorithms of DESeq2.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Spleen

extract_protocol: RNA was harvested using RNeasy micro kit (Qiagen). RNA libraries for RNA-seq were prepared using SMART-seq stranded kit (Takara) following manufacture's protocols.

value: Spleen


title: Preadipocyte-INPUT-rep02

city: Xi'an China

first: Renjie

last: Zhu

state: Shaanxi

address: No.28 Xianning West Road, Xi'an, Shaanxi 710049, P.R. China

department: School of Life Science and Technology

country: China

institute: Xi'an Jiaotong University

description:
PCR-free DNA
input sequencing library

data_processing:
Library strategy: STARR-seq
Each replicated sample paired reads were separated according to 8-bp barcode sequences
Low quality reads (Q-score<30) were removed using fastp 0.20.1
The 120-bp SNP element sequences were extracted and merged reads were aligned to our selected SNP sequences using Bowtie 2.4.1
All 100% matched reads were extracted and each SNP reference/alternative allele was counted according to unique UMI (removing PCR duplicates)
Genome_build: h19
Supplementary_files_format_and_content: Count.txt with raw reads counts for every SNP sequence and every sample

organism: synthetic construct

source_name: STARR-seq plasmid library

growth_protocol: The HepG2,A673 and preadipocyte cell lines were cultured in DMEM (HyClone) with 10% fetal bovine serum (Biological Industries), 100U/mL penicillin and 0.1 mg/mL streptomycin (Solarbio) at 37 °C, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using Monarch Total RNA Miniprep Kit (New England Biolabs), and treated with TURBO DNA-free Kit (Thermo Fisher) following the manufacturer’s protocol. We then isolated the poly(A) RNA using NEB Next Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and precipitated each replicate using Monarch RNA Cleanup Kit (New England Biolabs).
The plasmid library before transfection were used for constructing input sequencing library. Firstly, one-step PCR was performed with 100ng plasmid library using RT-UMI primer (unique random molecular identifiers, 5'-ACACGACGCTCTTCCGATCTNNNNNNNNNNNNNTCGAAGCGGCCGGCCGAATTCG-3').Then the first round of amplification was performed with Vector-F(5'-GCTAGGCTAGCAAAGGAGAAGAAC-3') and Read1-R (5'-ACACGACGCTCTTCCGATCT-3') for each replicate. The second round of PCR was performed using barcode primers for each biological replicate and further purified with Agencourt AMPure XP beads. For the output sequencing library, total RNA was extracted after plasmid library transfection. The poly(A) mRNA was reverse transcripted using RT-UMI primer and treated with RNase A. Next, the cDNA was amplified using junction primer (5'-TCGTGAGGCACTGGGCAG*G*T*G*T*C-3', * = phosphorothioate bond) and Read1-R. The second round of PCR was applied with barcode primers for each replicate and purified with Agencourt AMPure XP beads. Finally, input and output sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s recommendations and index codes were added for each sample.

treatment_protocol: The STARR-seq plasmid library was transfected into 1.0×10^7 cells for 24h according to manufacturer’s instructions, including A673, HepG2 and preadipocyte. Three biological replicates were performed for each cell line.

value: plasmid library before transfection


title: H1-derived microglia (stimulated) RNA-seq_rep2

data_processing:
Reads were trimmed to 51bp before aligning to hg19 genome assembly using STAR (v2.7.2b) with ENCODE recommended parameters
Gene expression levels (FPKM) were calculated using RSEM rsem-calculate-expression (v1.3.1) with gencode.v19 as annotation
Assembly: hg19
Supplementary files format and content: Tab-delimited text files of gene expression values for each sample
Supplementary files format and content: rsem.genes.results

extract_protocol:
RNA was extracted from fresh cells using the RNeasy Plus Mini Kit (Qiagen, 74134).
Approximately 1000 ng of extracted RNA was used to prepare libraries for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina, 20020594).

value: Microglia


title: Preadipocyte-INPUT-rep01

description:
PCR-free DNA
input sequencing library


title: cDC2_Cd47DT_2


title: HepG2-INPUT-rep03

description:
PCR-free DNA
input sequencing library


title: H1-derived microglia (stimulated) RNA-seq_rep1

value: stimulated


title: Hi-C siNIPBL replicate2


title: Hi-C siNIPBL replicate1


title: cDC2_Cd47DT_1


title: Hi-C siMau2

value: Mau2 siRNA


title: H1-derived microglia (resting) RNA-seq_rep2

value: H1 ESC-derived Microglia


title: Hi-C JQ1(+)

value: 1mM JQ1


title: HepG2-INPUT-rep02

description:
PCR-free DNA
input sequencing library


title: WTC11-derived microglia (stimulated) - ATAC_rep1

value: WTC11 iPSC-derived Microglia


title: cDC2_Cd47ff_3


title: Hi-C JQ1(-)

value: untreated


title: Trim33KO_HA_Recql_input


title: H1-derived microglia (resting) RNA-seq_rep1

value: resting


title: Preadipocyte-INPUT-rep03

description:
PCR-free DNA
input sequencing library


title: cDC2_Cd47ff_2


title: Hi-C siESCO1 replicate2

value: ESCO2 siRNA


title: HepG2-INPUT-rep01

description:
PCR-free DNA
input sequencing library


title: WTC11-derived microglia (stimulated) RNA-seq_rep2


title: cDC2_Cd47ff_1


title: WTC11-derived microglia (resting) - ATAC_rep1


title: A673-INPUT-rep03

description:
PCR-free DNA
input sequencing library


title: WTC11-derived microglia (stimulated) RNA-seq_rep1


title: A673-INPUT-rep02

description:
PCR-free DNA
input sequencing library


title: WTC11-derived microglia (resting) RNA-seq_rep2


title: Hi-C siESCO1 replicate1

value: ESCO1 siRNA


title: A673-INPUT-rep01

description:
PCR-free DNA
input sequencing library


title: Hi-C Control replicate6

value: mock


title: WTC11-derived microglia (resting) RNA-seq_rep1


title: Hi-C Control replicate4

value: MboI


title: Hi-C Control replicate3


title: Hi-C Control replicate5


title: Preadipocyte-OUTPUT-rep02

description:
PCR-free DNA
output sequencing library

source_name: preadipocyte cells

value: Adipose


title: Adrenal, control, GA102, WT4

city: Sendai, Miyagi

first: Shinichi

last: Sato

address: 1-1 Seiryo-machi, Aoba-ku

institute: Tohoku University Hospital

data_processing:
RaNA-Seq software was used to perform the FASTQ pre-processing (fastp 0.19.4) and quantification (salmon 0.9.1) of the samples
Assembly: Sheep, Ovis aries (Oar_v3.1)
Supplementary files format and content: Complete raw counts table
Supplementary files format and content: Normalized abundance measurements for all samples by TPMs
Supplementary files format and content: Differentially expressed gene were detected by DEseq2 R package and the Waid’s test.

organism: Ovis aries

source_name: Adrenal grand

extract_protocol:
RNA was extracted from the fetal adrenal gland using ISOSPIN Cell & Tissue RNA (catalog number 314-08211; Nippon Gene Co., Ltd., Tokyo, Japan) according to the manufacturer’s instructions.
Libraries were made using the NEBNext UltraTMⅡ Directional RNA Library Prep Kit (catalog number E7760; New England Biolabs, Inc., MA, USA)

value: Adrenal gland

tag: gestational age

value: 102 days

tag: Sex

value: male

value: saline solution was injected


title: Adrenal, control, GA102, WT5

value: female


title: Preadipocyte-OUTPUT-rep03

description:
PCR-free DNA
output sequencing library


title: Hi-C Control replicate2


title: HepG2-OUTPUT-rep03

description:
PCR-free DNA
output sequencing library

source_name: hepatocellular carcinomas cells

value: Liver


title: Preadipocyte-OUTPUT-rep01

description:
PCR-free DNA
output sequencing library


title: Hi-C Control replicate1


title: Adrenal, control, GA102, WT3


title: Adrenal, control, GA102, WT2


title: Adrenal, control, GA102, WT1


title: HepG2-OUTPUT-rep02

description:
PCR-free DNA
output sequencing library


title: Adrenal, endotoxin, GA102, LPS6

value: endotoxin was injected


title: Hi-C siCTCF (si626 and si628 double)

value: CTCF siRNA#1 & CTCF siRNA#2


title: HepG2-OUTPUT-rep01

description:
PCR-free DNA
output sequencing library


title: Hi-C siCTCF 120h

value: CTCF siRNA#1


title: Hi-C siCTCF 72h


title: Adrenal, endotoxin, GA102, LPS4


title: A673-OUTPUT-rep03

description:
PCR-free DNA
output sequencing library

source_name: rhabdomyoma cells

value: Muscle


title: Hi-C siCTCF replicate2


title: Adrenal, endotoxin, GA102, LPS3


title: A673-OUTPUT-rep02

description:
PCR-free DNA
output sequencing library


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving JKD_third biological replicate

type: RNA

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

country: Spain

institute: Center for Plant Biotechnology and Genomics

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-JKDc

hyb_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

label: biotin

organism: Arabidopsis thaliana

source_name: J0571 GFP sorted cells from excised root tips of plants from the line J0571 driving the expression of the JKD transcription factor at 5 days post imbibition

label_protocol: Affy two-cycle labeling (raw 21-26) and one-cycle (everything else) labeling protocol

growth_protocol: Standard media for 5 days

extract_protocol: Quiagen MicroRNAesy kit (total RNA was extracted according to the manufacturer's instruction

treatment_protocol: Root tips were collected

tag: ecotype

value: root tip

value: Seedling roots, 5 days after germination

tag: growth media


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving SCR_second biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-SCRb

scan_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

source_name: J0571 GFP sorted cells from excised root tips of plants from the line J0571 driving the expression of the SCR transcription factor at 5 days post imbibition

tag: tissue


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving JKD_first biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-JKDa

value: line J0571 driving the expression of the JKD transcription factor


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving SCR_third biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-SCRc

value: line J0571 driving the expression of the SCR transcription factor


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving JKD_second biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-JKDb


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving BLJ_third biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-BLJc

source_name: J0571 GFP sorted cells from excised root tips of plants from the line J0571 driving the expression of the BLJ transcription factor at 5 days post imbibition


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving SCR_first biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-SCRa


title: Hi-C siCTCF replicate1


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving BLJ_second biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-BLJb

value: line J0571 driving the expression of the BLJ transcription factor


title: A673-OUTPUT-rep01

description:
PCR-free DNA
output sequencing library


title: Adrenal, endotoxin, GA102, LPS2


title: 010-V323-EfficacyW17

status: Public on Jul 27 2023

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Alignment was performed using STAR version 2.5.2b
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count
Assembly: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf) (https://www.unmc.edu/rhesusgenechip/index.htm).
Supplementary files format and content: tab delimited text file containing  gene symbol and raw read counts for each sample (in columns) for each annotated transcript (in rows).

organism: Macaca mulatta

source_name: blood

extract_protocol:
Blood was collected at specified time points post 1st MVA immunization into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the PAXgene Blood RNA Kit IVD (Qiagen).
RNA quality was assessed using an Agilent Bioanalyzer and then one microgram of total RNA was subjected to globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific). Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio), which uses oligo-dT priming for the reverse transcription step. This process would yield low recovery of non-coding RNAs and hence we focused our analysis on protein coding transcripts. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina HiSeq3000 at 100SR, yielding 25-30 million reads per sample.

value: blood

tag: subject id

tag: vaccine route

value: IM

tag: timepoint


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_UAS driving BLJ_first biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571-BLJa


title: Adrenal, endotoxin, GA102, LPS5

value: Adrenal gland

tag: treatment


title: 010-V232-EfficacyW17


title: 010-V206-EfficacyW17


title: 010-RPe15-EfficacyW17

value: ID


title: 010-RHp16-EfficacyW17


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_third biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571c

source_name: J0571 GFP sorted cells from excised root tips of plants from the control line J0571 at 5 days post imbibition

value: control line J0571


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_first biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571a


title: 010-V208-EfficacyW17


title: 010-3_135-EfficacyW17


title: 010-RVs16-EfficacyW17


title: 010-V239-EfficacyW17


title: 010-V196-EfficacyW17


title: 010-RTr16-EfficacyW17


title: Arabidopsis ATH1_ground tissue marker_WT genetic background_second biological replicate

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
J0571b


title: 010-FD19-EfficacyW17


title: 010-K97-EfficacyW17


title: 010-RNs16-EfficacyW17


title: 010-DP5H-EfficacyW17


title: 010-GIM-EfficacyW17

value: GIM


title: 010-V232-EfficacyW16D4


title: 010-V206-EfficacyW16D4


title: 010-V323-EfficacyW16D4


title: 010-V196-EfficacyW16D4


title: 010-RVs16-EfficacyW16D4


title: 010-GIM-EfficacyW16D4


title: 010-RPe15-EfficacyW16D4


title: 010-3_135-EfficacyW16D4


title: 010-RHp16-EfficacyW16D4


title: 010-DV2E-EfficacyW16D4


title: 010-V239-EfficacyW16D4


title: 010-DV2E-EfficacyW17


title: 010-RTr16-EfficacyW16D4


title: 010-100_12-EfficacyW17


title: 010-K97-EfficacyW16D4


title: 010-RNs16-EfficacyW16D4


title: 010-RHf53-EfficacyW16D4


title: 010-DP5H-EfficacyW16D4


title: 010-100_12-EfficacyW16D4


title: 010-FD19-EfficacyW16D4


title: 010-V323-EfficacyW16D2


title: 010-V206-EfficacyW16D2


title: 010-V232-EfficacyW16D2


title: 010-RHp16-EfficacyW16D2


title: 010-RPe15-EfficacyW16D2


title: 010-DV2E-EfficacyW16D2


title: 010-3_135-EfficacyW16D2


title: 010-V239-EfficacyW16D2


title: 010-V196-EfficacyW16D2


title: 010-V208-EfficacyW16D2


title: 010-V200-EfficacyW16D2


title: 010-RNs16-EfficacyW16D2


title: 010-K97-EfficacyW16D2


title: 010-RTr16-EfficacyW16D2


title: 010-V208-EfficacyW16D4


title: 010-V200-EfficacyW16D4


title: 010-RHf53-EfficacyW16D2


title: 010-DP5H-EfficacyW16D2


title: 010-V206-EfficacyW16D1


title: 010-V232-EfficacyW16D1


title: 010-V323-EfficacyW16D1


title: 010-100_12-EfficacyW16D2


title: 010-RHp16-EfficacyW16D1


title: 010-RPe15-EfficacyW16D1


title: 010-V196-EfficacyW16D1


title: 010-DV2E-EfficacyW16D1


title: 010-RTr16-EfficacyW16D1


title: 010-V208-EfficacyW16D1


title: 010-V200-EfficacyW16D1


title: 010-V239-EfficacyW16D1


title: 010-RHf53-EfficacyW16D1


title: 010-FD19-EfficacyW16D2


title: 010-K97-EfficacyW16D1


title: 010-FD19-EfficacyW16D1


title: 010-V323-EfficacyW16


title: 010-V232-EfficacyW16


title: 010-100_12-EfficacyW16D1


title: 010-DP5H-EfficacyW16D1


title: 010-RVs16-EfficacyW16


title: 010-V196-EfficacyW16


title: 010-RPe15-EfficacyW16


title: Trim33KO_HA_Recql_HU_HA

source_name: liver

value: liver

tag: cell line

tag: cell type

value: HCC

tag: genotype

value: HU

value: anti-HA


title: 010-V206-EfficacyW16


title: 010-GIM-EfficacyW16D1


title: 010-3_135-EfficacyW16D1


title: 010-RHp16-EfficacyW16


title: 010-3_135-EfficacyW16


title: 010-RNs16-EfficacyW16D1


title: 010-V239-EfficacyW16


title: 010-V208-EfficacyW16


title: 010-V200-EfficacyW16


title: 010-DV2E-EfficacyW16


title: 010-RNs16-EfficacyW16


title: 010-FD19-EfficacyW16


title: 010-RTr16-EfficacyW16


title: 010-100_12-EfficacyW16


title: 010-RHf53-EfficacyW16


title: qPRO_RedS_Bioreplicate 2

city: Staten Island

first: Cesar

last: Arenas-Mena

state: New York

address: 2800 Victory Boulevard

department: Biology

institute: CSI CUNY

description:
Quick PRO-seq
P_RSC_22_1_2_minus3.rpm.bw
P_RSC_22_1_2_plus3.rpm.bw
RSC_22.dREG.peak.prob_100_merged_sort.bed

data_processing:
Read map and data processing as in (Arenas-Mena et. al, 2021)
Assembly: Sp5.0  https://www.ncbi.nlm.nih.gov/assembly/GCF_000002235.5/
Library strategy: PRO-seq and Quick-PRO-seq

organism: Strongylocentrotus purpuratus

source_name: 8 hour hatching blastula embryos

growth_protocol: 15 degrees Celsius

extract_protocol:
Density gradient nuclear prep (Arenas-Mena et. al, 2021) https://doi.org/10.1186/s12864-021-07936-0
PRO-seq (Arenas-Mena et. al, 2021) https://doi.org/10.1186/s12864-021-07936-0. Quick PRO-seq (Judd et. al, 2020)  https://www.protocols.io/view/a-rapid-sensitive-scalable-method-for-precision-ru-57dg9i6.pdf

value: 8 hour hatching blastula embryos

value: Wild


title: qPRO_72h_Bioreplicate 1

description:
Quick PRO-seq
P_72h_22_minus3.rpm.bw
P_72h_22_plus3.rpm.bw


title: Omni-ATAC_RedS

description:
ATAC_RSCoT1_1_RSCoT2_1_merged_RPM.bw
RSCo_T1_T2_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak.gz

data_processing:
ENCOCE-DCC atac-seq-pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) default parameters
MACS2 peak call p threshold set to 0.05.
Library normalization of merged biological replicates to reads per million (rpm).
Assembly: Sp5.0  https://www.ncbi.nlm.nih.gov/assembly/GCF_000002235.5/

source_name: Red Spherule Cells

extract_protocol:
Nuclear preps, ATAC-seq in embryos and larvae followed previously stablished protocols (Arenas-Mena et al., 2021) https://doi.org/10.1186/s12864-021-07936-0, except that for red spherule cells the lysis buffer during the nuclear prep was supplemented with 0.1 % NP40, 0.1% Tween-20, and 1% BSA, and the density gradient solutions were supplemented with 1% BSA to diminish nuclear shearing. Red spherule cells were purified from the coelomic fluid of adult sea urchins following a previously stablished method (Smith et al., 2019).  OmniATAC in 72 hour embryos raised at 15 degrees C and red spherule cells was performed as previously described (Corces et al., 2017).
ATAC-seq (Arenas-Mena et. al, 2021) https://doi.org/10.1186/s12864-021-07936-0. Omni-ATAC protocol followed previously stablished protocol (Corces et. al, 2017) https://doi.org/10.1038/nmeth.4396

value: Red Spherule Cells


title: PRO_8h_Bioreplicate 1.2

description:
PRO-seq
8h_5.0_minus3.rpm.bw
8h_5.0_plus3.rpm.bw
8h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: PRO_72h_Bioreplicate 2

description:
PRO-seq
72h_5.0_minus3.rpm.bw
72h_5.0_plus3.rpm.bw
72h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: 010-GIM-EfficacyW16


title: PRO_8h_Bioreplicate 1.1


title: qPRO_72h_Bioreplicate 2


title: ATAC_RedSn_Bioreplicate 2

description:
ATAC_RSCnB1_1_RSCnB2_1_merged_sort_RPM.bw
RSCn_B1_B2_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed


title: PRO_72h_Bioreplicate 1


title: ATAC_RedSn_Bioreplicate 1


title: ATAC_72h_Bioreplicate 1

description:
ATAC_72h19_72h_72M__merged_RPM.bw
72h19_72h_72hM_2022_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed

source_name: 72 hour embryos

value: 72 hour embryos


title: ATAC_72h_Bioreplicate 2


title: Omni-ATAC_72h_Bioreplicate 2

description:
A_72h_22_1_72h_22_2_merged_sort_RPM.bw
A_72_22.pooled.pval0.01.300K.narrowPeak_sort_merge.bed


title: ATAC_20h_Bioreplicate 1

description:
ATAC_20h1_1_20h2_1.merged.sort_RPM.bw
20h_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed

source_name: 20 hour embryos

value: 20 hour embryos


title: ATAC_20h_Bioreplicate 2


title: Omni-ATAC_72h_Bioreplicate 1


title: 010-K97-EfficacyW16


title: ATAC_4C_Bioreplicate 2

description:
ATAC_8C5h7_4CD227A8_merged_sort_RPM.bw
8C_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed

source_name: 4 Cell embryos

value: 4 Cell embryos


title: cell_Q5_S149

city: Boston

first: VICTOR

last: BARRERA BURGOS

state: Massachusetts

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

description: NextSeq Mid 2 X 75 per flow

library_source: transcriptomic single cell

data_processing:
Raw reads were examined for quality issues using FastQC
Sequenced reads were trimmed for adaptor sequence (if required) using Cutadapt
Trimmed reads were aligned to the UCSC genome mm10 using salmon
Counts of reads aligning to known genes were generated by tximport.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files for raw counts

source_name: CD1 mice, strain  #022 from Charles River

extract_protocol:
We used 18 amplification cycles, and the cells were split up in 5 cDNA synthesis batches with 16-36 cells per round. cDNA was purified after amplification using Agencourt AMPure XP beads (Beckman Coulter #A63880).
The DNA libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina # FC-131-1024).

tag: strain

value: somatosensory neuron

tag: classification

value: hairy

tag: litter

tag: library

tag: plate


title: cell_Q6_S150

description: NextSeq Mid 2 X 75 per flow

value: CD1 mice, strain  #022 from Charles River

tag: age


title: cell_Q3_S147

description: NextSeq Mid 2 X 75 per flow


title: qPRO_RedS_Bioreplicate 1


title: cell_Q4_S148

description: NextSeq Mid 2 X 75 per flow

value: glabrous


title: ATAC_4C_Bioreplicate 1

source_name: 4 Cell  embryos

value: 4 Cell  embryos


title: cell_P8_S136

description: NextSeq Mid 2 X 75 per flow


title: cell_P7_S135

description: NextSeq Mid 2 X 75 per flow


title: cell_Q1_S145

description: NextSeq Mid 2 X 75 per flow


title: cell_P9_S137

description: NextSeq Mid 2 X 75 per flow


title: cell_Q2_S146

description: NextSeq Mid 2 X 75 per flow


title: cell_P3_S131

description: NextSeq Mid 2 X 75 per flow


title: cell_P6_S134

description: NextSeq Mid 2 X 75 per flow


title: cell_P2_S130

description: NextSeq Mid 2 X 75 per flow


title: cell_P4_S132

description: NextSeq Mid 2 X 75 per flow


title: cell_P5_S133

description: NextSeq Mid 2 X 75 per flow


title: ATAC_8h_Bioreplicate 2

description:
ATAC_8h521_ATAC8h529_RPM.bw
8h_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed

source_name: 8 hour embryos

value: 8 hour embryos


title: cell_P13_S141

description: NextSeq Mid 2 X 75 per flow


title: ATAC_8h_Bioreplicate 1


title: cell_P14_S142

description: NextSeq Mid 2 X 75 per flow


title: cell_P16_S144

description: NextSeq Mid 2 X 75 per flow


title: cell_P12_S140

description: NextSeq Mid 2 X 75 per flow


title: cell_P11_S139

description: NextSeq Mid 2 X 75 per flow


title: cell_P15_S143

description: NextSeq Mid 2 X 75 per flow


title: cell_P1_S129

description: NextSeq Mid 2 X 75 per flow


title: cell_O9_S128

description: NextSeq Mid 2 X 75 per flow

value: O


title: 010-DP5H-EfficacyW16

value: blood

value: ID


title: cell_O3_S122

description: NextSeq Mid 2 X 75 per flow


title: cell_O6_S125

description: NextSeq Mid 2 X 75 per flow


title: cell_O7_S126

description: NextSeq Mid 2 X 75 per flow


title: cell_O4_S123

description: NextSeq Mid 2 X 75 per flow


title: cell_O5_S124

description: NextSeq Mid 2 X 75 per flow


title: cell_O8_S127

description: NextSeq Mid 2 X 75 per flow


title: cell_M8_S119

description: NextSeq Mid 2 X 75 per flow

value: M


title: cell_O2_S121

description: NextSeq Mid 2 X 75 per flow


title: cell_O1_S120

description: NextSeq Mid 2 X 75 per flow


title: cell_M7_S118

description: NextSeq Mid 2 X 75 per flow


title: cell_M6_S117

description: NextSeq Mid 2 X 75 per flow


title: cell_M5_S116

description: NextSeq Mid 2 X 75 per flow


title: cell_M4_S115

description: NextSeq Mid 2 X 75 per flow


title: cell_M2_S113

description: NextSeq Mid 2 X 75 per flow


title: cell_M3_S114

description: NextSeq Mid 2 X 75 per flow


title: cell_M1_S112

description: NextSeq Mid 2 X 75 per flow


title: cell_P10_S138

description: NextSeq Mid 2 X 75 per flow


title: cell_L5_S108

description: NextSeq Mid 2 X 75 per flow

value: L


title: cell_L6_S109

description: NextSeq Mid 2 X 75 per flow


title: cell_L7_S110

description: NextSeq Mid 2 X 75 per flow


title: cell_L2_S105

description: NextSeq Mid 2 X 75 per flow


title: cell_L4_S107

description: NextSeq Mid 2 X 75 per flow


title: cell_L1_S104

description: NextSeq Mid 2 X 75 per flow


title: 010-RHf53-EfficacyW17


title: cell_K9_S101

description: NextSeq Mid 2 X 75 per flow

value: K


title: cell_K8_S100

description: NextSeq Mid 2 X 75 per flow


title: cell_L8_S111

description: NextSeq Mid 2 X 75 per flow


title: cell_L3_S106

description: NextSeq Mid 2 X 75 per flow


title: cell_K6_S98

description: NextSeq Mid 2 X 75 per flow


title: cell_K5_S97

description: NextSeq Mid 2 X 75 per flow


title: cell_K4_S96

description: NextSeq Mid 2 X 75 per flow


title: cell_K3_S95

description: NextSeq Mid 2 X 75 per flow


title: cell_K2_S94

description: NextSeq Mid 2 X 75 per flow


title: cell_K11_S103

description: NextSeq Mid 2 X 75 per flow


title: cell_K7_S99

description: NextSeq Mid 2 X 75 per flow


title: cell_K10_S102

description: NextSeq Mid 2 X 75 per flow


title: cell_I7_S68

description: NextSeq Mid 2 X 75 per flow

value: I


title: cell_K1_S93

description: NextSeq Mid 2 X 75 per flow


title: cell_I8_S69

description: NextSeq Mid 2 X 75 per flow


title: cell_I5_S66

description: NextSeq Mid 2 X 75 per flow


title: cell_I4_S65

description: NextSeq Mid 2 X 75 per flow


title: cell_I32_S92

description: NextSeq Mid 2 X 75 per flow


title: cell_I6_S67

description: NextSeq Mid 2 X 75 per flow


title: cell_I29_S89

description: NextSeq Mid 2 X 75 per flow


title: cell_I3_S64

description: NextSeq Mid 2 X 75 per flow


title: cell_I31_S91

description: NextSeq Mid 2 X 75 per flow


title: cell_I26_S86

description: NextSeq Mid 2 X 75 per flow


title: cell_I30_S90

description: NextSeq Mid 2 X 75 per flow


title: cell_I27_S87

description: NextSeq Mid 2 X 75 per flow


title: cell_I25_S85

description: NextSeq Mid 2 X 75 per flow


title: cell_I22_S83

description: NextSeq Mid 2 X 75 per flow


title: cell_I28_S88

description: NextSeq Mid 2 X 75 per flow


title: cell_I24_S84

description: NextSeq Mid 2 X 75 per flow


title: cell_I21_S82

description: NextSeq Mid 2 X 75 per flow


title: cell_I20_S81

description: NextSeq Mid 2 X 75 per flow


title: cell_I2_S63

description: NextSeq Mid 2 X 75 per flow


title: cell_I17_S78

description: NextSeq Mid 2 X 75 per flow


title: cell_I16_S77

description: NextSeq Mid 2 X 75 per flow


title: cell_I19_S80

description: NextSeq Mid 2 X 75 per flow


title: cell_I15_S76

description: NextSeq Mid 2 X 75 per flow


title: cell_I14_S75

description: NextSeq Mid 2 X 75 per flow


title: cell_I13_S74

description: NextSeq Mid 2 X 75 per flow


title: cell_I1_S62

description: NextSeq Mid 2 X 75 per flow


title: cell_I11_S72

description: NextSeq Mid 2 X 75 per flow


title: cell_I10_S71

description: NextSeq Mid 2 X 75 per flow


title: cell_h9_S59

description: NextSeq Mid 2 X 75 per flow

value: H


title: cell_I9_S70

description: NextSeq Mid 2 X 75 per flow


title: cell_h5_S56

description: NextSeq Mid 2 X 75 per flow


title: cell_h2_S54

description: NextSeq Mid 2 X 75 per flow


title: cell_h4_S55

description: NextSeq Mid 2 X 75 per flow


title: cell_h12_S61

description: NextSeq Mid 2 X 75 per flow


title: cell_g9_S51

description: NextSeq Mid 2 X 75 per flow


title: cell_h11_S60

description: NextSeq Mid 2 X 75 per flow


title: cell_h1_S53

description: NextSeq Mid 2 X 75 per flow


title: cell_g3_S45

description: NextSeq Mid 2 X 75 per flow


title: cell_g5_S47

description: NextSeq Mid 2 X 75 per flow


title: cell_g7_S49

description: NextSeq Mid 2 X 75 per flow


title: cell_g8_S50

description: NextSeq Mid 2 X 75 per flow


title: cell_g4_S46

description: NextSeq Mid 2 X 75 per flow


title: cell_g10_S52

description: NextSeq Mid 2 X 75 per flow


title: cell_g1_S43

description: NextSeq Mid 2 X 75 per flow


title: cell_f8_S31

description: NextSeq Mid 2 X 75 per flow


title: cell_f7_S30

description: NextSeq Mid 2 X 75 per flow


title: cell_f6_S29

description: NextSeq Mid 2 X 75 per flow


title: cell_I12_S73

description: NextSeq Mid 2 X 75 per flow


title: cell_h8_S58

description: NextSeq Mid 2 X 75 per flow


title: cell_f4_S27

description: NextSeq Mid 2 X 75 per flow


title: cell_h7_S57

description: NextSeq Mid 2 X 75 per flow


title: cell_f2_S25

description: NextSeq Mid 2 X 75 per flow


title: cell_f5_S28

description: NextSeq Mid 2 X 75 per flow


title: cell_f3_S26

description: NextSeq Mid 2 X 75 per flow


title: cell_f12_S35

description: NextSeq Mid 2 X 75 per flow


title: cell_f11_S34

description: NextSeq Mid 2 X 75 per flow


title: cell_g2_S44

description: NextSeq Mid 2 X 75 per flow


title: cell_f10_S33

description: NextSeq Mid 2 X 75 per flow


title: cell_e7_S23

description: NextSeq Mid 2 X 75 per flow


title: cell_g6_S48

description: NextSeq Mid 2 X 75 per flow


title: cell_f1_S24

description: NextSeq Mid 2 X 75 per flow


title: cell_e5_S21

description: NextSeq Mid 2 X 75 per flow


title: cell_e9_S36

description: NextSeq Mid 2 X 75 per flow


title: cell_e6_S22

description: NextSeq Mid 2 X 75 per flow


title: cell_e15_S41

description: NextSeq Mid 2 X 75 per flow


title: cell_e4_S20

description: NextSeq Mid 2 X 75 per flow


title: cell_e2_S18

description: NextSeq Mid 2 X 75 per flow


title: cell_e3_S19

description: NextSeq Mid 2 X 75 per flow


title: cell_f9_S32

description: NextSeq Mid 2 X 75 per flow


title: cell_e12_S39

description: NextSeq Mid 2 X 75 per flow


title: cell_e13_S40

description: NextSeq Mid 2 X 75 per flow


title: cell_e16_S42

description: NextSeq Mid 2 X 75 per flow


title: dhh1-2

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Reads were trimmed using Trim Galore
Reads were mapped on the S. cerevisiae reference genome (R64-2-1, including the 2-micron plasmid) and ERCC spike-in RNA sequences, using HISAT2 V2.2.0, with default parameters and maximum intron size of 5000.
Gene count was obtained with featureCounts v2.0.0.
Gene count was normalized using estimatesizefactorsformatrix() function from DESeq2 package (R software), using snoRNA counts.
Normalized densities were computed for each sample as: normalized gene count / gene length
Assembly: R64-2-1
Supplementary files format and content: tab delimited file, containing normalized tag/nt for each sample

organism: Saccharomyces cerevisiae

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ dhh1::kanMX4

growth_protocol: Yeast cells were grown to mid-log phase (OD600 0.5) at 30°C in YPD medium.

extract_protocol:
Total RNA was extracted from cells grown to mid-log phase (OD600 0.5) using standard hot phenol procedure. Extracted RNA was ethanol-precipitated, resuspended in nuclease-free H2O (Ambion) and quantified using a NanoDrop 2000c spectrophotometer and/or a Qubit fluorometer with the Qubit RNA HS Assay kit (Life Technologies)
RNA-seq libraries were prepared from 50 ng of rRNA-depleted RNAs using the TruSeq Stranded mRNA kit (Illumina)

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta} dhh1{delta}::kanMX4


title: dhh1-1


title: cell_e11_S38

description: NextSeq Mid 2 X 75 per flow


title: cell_e1_S17

description: NextSeq Mid 2 X 75 per flow


title: cell_D6_S15

description: NextSeq Mid 2 X 75 per flow


title: dbp1-1

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ dbp1::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta} dbp1{delta}::kanMX4


title: dbp1-2


title: ski2-2

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ ski2::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta} ski2{delta}::kanMX4


title: cell_D5_S14

description: NextSeq Mid 2 X 75 per flow

value: somatosensory neuron


title: cell_D4_S13

description: NextSeq Mid 2 X 75 per flow

value: hairy


title: ski2-1


title: cell_D1_S12

description: NextSeq Mid 2 X 75 per flow

value: CD1 mice, strain  #022 from Charles River


title: slh1-2

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ slh1::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta} slh1{delta}::kanMX4


title: cell_C6_S10

description: NextSeq Mid 2 X 75 per flow

value: glabrous


title: cell_C5_S9

description: NextSeq Mid 2 X 75 per flow


title: slh1-1


title: cell_C1_S7

description: NextSeq Mid 2 X 75 per flow


title: cell_e10_S37

description: NextSeq Mid 2 X 75 per flow


title: ecm32-2

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ ecm32::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta} ecm32{delta}::kanMX4


title: ecm32-1


title: cell_C7_S11

description: NextSeq Mid 2 X 75 per flow


title: cell_C4_S8

description: NextSeq Mid 2 X 75 per flow


title: WT-1

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: cell_D7_S16

description: NextSeq Mid 2 X 75 per flow


title: WT-2


title: cell_B4_S6

description: NextSeq Mid 2 X 75 per flow


title: cell_B2_S5

description: NextSeq Mid 2 X 75 per flow


title: cell_B1_S4

description: NextSeq Mid 2 X 75 per flow


title: cell_A7_S3

description: NextSeq Mid 2 X 75 per flow


title: cell_A1_S1

description: NextSeq Mid 2 X 75 per flow


title: cell_A6_S2

description: NextSeq Mid 2 X 75 per flow


title: Sample_Wt_350

city: Augusta

first: Joseph

last: Miano

address: 1460 Laney Walker Blvd, CL-3060

institute: Medical College of Georgia at Augusta University

data_processing:
Data Formatting bcltofastq-2.19.0
Data Cleaning Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome Alignment STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification 1 subread-1.6.1, featurecounts, -s 2 -t exon -g gene_name
Read Quantification 2 subread-1.6.1, featurecounts, -M -s 2 -t exon -g gene_name
Assembly: GRCm38 + gencode M17
Supplementary files format and content: tab-delimited  text file of gene counts

source_name: Aorta

extract_protocol:
Aortae snap frozen in liquid nitrogen, pulverized in TRIzol, and extracted per Manufacturer's protocol
RNA libraries for RNA-seq were prepared using Truseq Stranded Total RNA Library Prep Kit following manufacturer's protocols.

value: Aorta

value: Cnn1 wild type


title: Sample_Mut_359

value: Cnn1 KO


title: Sample_Mut_358


title: Sample_Wt_357


title: Sample_Mut_365


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2, rep3

city: Mainz

first: Stefanie

last: Ebersberger

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with non-default parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcodes.fasta (using sample barcodes: in vitro oligo library, 50nM U2AF2, rep1: NNNNNCGTGATNNNN; in vitro oligo library, 50nM U2AF2, rep2: NNNNNACATCGNNNN; in vitro oligo library, 50nM U2AF2, rep3: NNNNNGCCTAANNNN; in vitro oligo library, 50nM U2AF2 + 50nM FUPB1, rep1: NNNNNTGGTCANNNN; in vitro oligo library, 50nM U2AF2 + 50nM FUPB1, rep2: NNNNNCACTGTNNNN; in vitro oligo library, 50nM U2AF2 + 50nM FUPB1, rep3: NNNNNATTGGCNNNN; in vitro oligo library, 50nM U2AF2 + 300nM FUPB1, rep1: NNNNNGATCTGNNNN; in vitro oligo library, 50nM U2AF2 + 300nM FUPB1, rep2: NNNNNTCAAGTNNNN; in vitro oligo library, 50nM U2AF2 + 300nM FUPB1, rep3: NNNNNCTGATCNNNN; in vitro transcript library, 50nM U2AF2, rep1: NNNNNCGTGATNNNN; in vitro transcript library, 50nM U2AF2, rep2: NNNNNACATCGNNNN; in vitro transcript library, 50nM U2AF2, rep3: NNNNNGCCTAANNNN; in vitro transcript library, 50nM U2AF2 + 50nM FUBP1, rep1: NNNNNTGGTCANNNN; in vitro transcript library, 50nM U2AF2 + 50nM FUBP1, rep2: NNNNNCACTGTNNNN; in vitro transcript library, 50nM U2AF2 + 50nM delta N-term FUBP1, rep1: NNNNNTCAAGTNNNN; in vitro transcript library, 50nM U2AF2 + 50nM delta N-term FUBP1, rep2: NNNNNCTGATCNNNN; in vitro transcript library, 50nM U2AF2 + 50nM N-term FUBP1, rep1: NNNNNATTGGCNNNN; in vitro transcript library, 50nM U2AF2 + 50nM N-term FUBP1, rep2: NNNNNGATCTGNNNN)
Mapping: STAR (v2.6.1b) with non-default parameters: --genomeDir Gencode_release31_GRCh38.p12 --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --sjdbOverhang 134 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate
Duplicate removal: UMI-tools (v1.0.0) with non-default parameter: umi_tools dedup --method unique
BAM to BED shifting one base upstream: bedtools (v2.27.1): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.27.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
Normalized bw files are obtained by dividing the signal per nucleotide by a scaling factor which is the ratio of the maximum of the total count of all spike-ins over all libraries divided by the total count of all spike-ins per library
Assembly: GRCh38.p12 (Gencode release 31)
Supplementary files format and content: bigWig (crosslink events per nucleotide)

source_name: in vitro oligo library

extract_protocol:
In vitro iCLIP measures the intrinsic binding affinity of a given RBP.  Recombinant protein and minigene in vitro transcripts (PMID: 29643205) or a large-scale oligo library are mixed and subjected to crosslinking and immunoprecipitation of the RBP of interest. For all in vitro iCLIPs, the in vitro transcript pool or oligo library was preheated for 5 min at 70°C to minimise RNA secondary structures.For minigene in vitro iCLIP, a final concentration of 2 nM of in vitro transcript pool were added to 50 nM U2AF2 RRM12 alone, or to 50 nM U2AF2 RRM12 supplemented with either 50 nM of FUBP1FL, FUBP1ΔN, or FUBP1N74 (imb_koenig_2018_01_sub12). The mixtures were incubated at 37°C for 5 min before UV-irradiation (50 mJ/cm^2). Minigene in vitro iCLIP was spiked with 10 µl crosslinked mixture containing 250 nM U2AF2RRM12 and 6 nM NUP133 in vitro transcript for normalisation.For the oligo in vitro iCLIP, the large-scale oligo library of 200mers was used. Here, 50 nM of the oligo library was incubated with 50 nM U2AF2 RRM12 alone or with either 50 nM or 300 nM FUBP1 (imb_koenig_2018_01_sub16). The mixtures were incubated at 37°C for 5 min before UV-irradiation (50 mJ/cm^2). Partial RNase digestion and L3 linker ligation was skipped as they do not apply here. Oligo in vitro iCLIP was spiked with a mix of ten 150 nt long spike-in oligonucleotides for normalisation.
Reverse Transcription and library generation was performed according to the iCLIP2 protocol (PMID: 31610236). In vitro iCLIP libraries were sequenced on an Illumina NextSeq 500 sequencing machine as 150 nt single-end reads including a 6 nt sample barcode as well as 5+4 nt unique molecular identifiers (UMIs).

value: in vitro oligo library

tag: chip antibody

tag: agent

value: 50nM U2AF2


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2 + 50nM delta N FUBP1, rep1

value: 50nM U2AF2 + 50nM delta N FUBP1


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2 + 50nM N74 FUBP1, rep2

value: 50nM U2AF2 + 50nM N74 FUBP1


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2 + 50nM N74 FUBP1, rep1


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2 + 300nM FUPB1, rep2

value: 50nM U2AF2 + 300nM FUPB1


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2 + 50nM FUPB1, rep1

value: 50nM U2AF2 + 50nM FUPB1


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2 + 50nM FUBP1, rep1

value: 50nM U2AF2 + 50nM FUBP1


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2 + 50nM FUPB1, rep3


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2 + 50nM FUBP1, rep2


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2 + 300nM FUPB1, rep1


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2, rep3


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2 + 50nM delta N FUBP1, rep2


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2, rep1


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2 + 50nM FUPB1, rep2


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2 + 300nM FUPB1, rep3


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2, rep1


title: imb_koenig_2018_01_sub12, in vitro oligo library, 50nM U2AF2, rep2


title: Sample_Wt_217


title: 010-V200-EfficacyW17

source_name: blood

value: blood

value: IM


title: Tannerella forsythia infected 16 weeks Female Mice 8

city: gainesville

first: Kesavalu

middle: Lakshmyya

last: Naidu

state: Florida

address: 1600 SW Archer Road

department: Dentistry

institute: University of Florida

hyb_protocol: We used high-throughput nCounter® miRNA Expression Panels (Nanostring Technologies, Seattle, WA, USA) to effectively identify the DE of miRNA in both sexes. Nanos-  Int. J. Mol. Sci. 2022, 23, 5107 14 of 18  tring nCounter® analysis can identify 577 miRNAs in any sample, and by using molecular  barcodes, it can detect even a low number of miRNAs without the need for reverse transcription or amplification.  miRNA expression profiling was performed using the Nanostring nCounter® Mouse  miRNA Assay kit v1.5 (Nanostring Technologies). This assay is a highly sensitive multiplexed method that detects miRNAs using molecular barcodes called nCounter reporter  probes without the need for reverse transcription. Sample preparation involved annealing,  ligation, and purification. These steps were carried out based on the experimental procedure described in the nCounter® miRNA assay panel kit. Briefly, the annealing master  mix was prepared by combining 13 µL of annealing buffer, 26 µL of nCounter miRNA Tag  reagent, and 6.5 of diluted (1:500) miRNA assay controls. Next, 3.5 µL of the annealing master mix was aliquoted into each tube of the strip tube and 100 ng of the total RNA from six  left mandibles from each group (maximum 3-µL volume) with 260/280 and 260/230 ratios  of greater than 2 was added to the respective tubes. The strip tube was placed in the  Thermal Cycler with the following conditions: 94 ◦C for 1 min, 65 ◦C for 1 min, 45 ◦C for  1 min, and 48 ◦C for hold.  After annealing, 2.5 µL of the ligation master mix (19.5 µL of polyethylene glycol (PEG)  and 13 µL of ligation buffer) was added to all the tubes in the strip tube. The strip tube  was incubated at 48 ◦C for 5 min, followed by the addition of 1 µL of ligase into each tube  without removing the strip tubes from the Thermal Cycler. Ligation was performed with  the following conditions: 48 ◦C for 3 min, 47 ◦C for 3 min, 46 ◦C for 3 min, 45 ◦C for 3 min,  65 ◦C for 10 min, and 4 ◦C for hold. To remove the unligated tags, a purification step was  performed after adding 1 µL of ligation cleanup enzyme to all the tubes and incubating the  tubes at 37 ◦C for 1 h, 70 ◦C for 10 min, and 4 ◦C for hold. Forty microliters of RNase-free  water were added to each tube in the strip tube and the sample was ready for hybridization  with the nCounter reporter and capture probes. After denaturation at 85 ◦C for 5 min, a  5-µL aliquot from the miRNA sample preparation tube was taken along with the 10 µL of  miRNA reporter code, 10 µL of hybridization buffer, and 5 µL miRNA capture probe. The  strip tubes were incubated at 65 ◦C for 18 h in the Thermal cycler, and the samples were  immediately processed for post-hybridization with the nCounter analysis system at the  Molecular Pathology Core at the University of Florida.  The nCounter® Mouse miRNA Assay kit v1.5 provided six positive hybridization controls and eight negative control probes to monitor hybridization efficiency. All components  and reagents needed for sample preparation at the reparation station were taken from  the nCounter master kit (Nanostring Technologies). Twelve samples per cartridge were  processed in a single run, which took 3 h. This was followed by digital analysis, which  involved the transfer of the cartridge to the multichannel epifluorescence digital analyzer.  A cartridge definition file with a maximum fields of view (FOV) count of 555 per flow cell  was taken for digital analysis. The number of images taken per scan corresponded to the  number of immobilized reporter probes on the cartridge. A separate Reporter Code Count  (RCC) file for each sample containing the count for each probe was downloaded and used  for data analysis.

data_processing: Initial data analysis was performed using nSolver 4.0. Initially, RCC files were imported into nSolver and imaging quality control (QC), binding density QC, positive control linearity QC, and positive control limit of detection QC were carried out as recommended in the system QC parameters. The lanes were flagged when the percent FOV registration was less than 75% for imaging QC. Binding density was outside the range from 0.1 to 2.25 for binding density QC, and the positive control R2 value was less than 0.95. All 24 samples passed the QC, and no flag lanes were observed. Raw data were generated after passing the QC. To reduce the background signal/noise, the background threshold count value was set to 52 and calculated by taking an average of eight negative control probe counts from all 24 samples. Codeset content normalization parameters were chosen, and the normalization was performed based on the top 100 miRNA genes expressed. The normalized factor was calculated based on the geometric mean values of the miRNA genes expressed in each sample. Fold changes in the genes were calculated based on the ratio of the difference in the means of the log-transformed normalized data to the square root of the sum of the variances of the samples in the two groups. The limma R library was used to calculate fold changes. Clustering of miRNA for the final heatmap of DE miRNA was done using the Partitioning Around Medoids method with the fpc R library.

source_name: Infected 16 weeks

growth_protocol: Tannerella forsythia ATCC 43037 (Tf) was grown in tryptic soy broth supplemented with N-acetyl muramic acid (5 mg/mL) and hemin (1 mg/mL) for three days in anaerobic growth chamber.

extract_protocol: Total RNA isolated from the mandible tissue using mirVana miRNA isolation kit (Ambion, Austin, TX, USA). mandibles from each mouse were entirely homogenized using the handheld rotor-stator homogenizer with sterile individual TissueRuptor disposable probes (Qiagen; Germantown, MD, USA) for each sample. After homogenization, each sample was lysed in a denaturing lysis solution that stabilized RNAs and inactivated RNases. The samples were subjected to an acid-phenol:chloroform extraction that removed all the cellular components such as protein, DNA, and other cellular products. The aqueous phase was removed, transferred to the fresh nuclease-free microcentrifuge tube, and 1.25 volume of 100% ethanol was added. This mixture was transferred to the filter cartridge placed into the collection tube and centrifuged for 15 s at 10,000× g. The filter cartridge was washed with 700 µL of wash solution-1 followed by washing with wash solution-2/3. After washing, the total RNA was eluted from the filter cartridge with 100 µL of nuclease-free water. RNA yield and purity were determined using a Take3 micro-volume plate in Epoch Microplate Spectrophotometer (BioTek), and quantification was performed in technical duplicates for each sample.

treatment_protocol: 100 million bacterial cells suspended in reduced transport fluid is mixed with equal volume of 6% carboxymethylcellulose (CMC) and administed orally. 0.1 ml cell suspension/mice.

tag: gender

value: female

value: Left Mandibles

value: infected with Tannerella forsythia

tag: time point

value: 23 weeks


title: Tannerella forsythia infected 16 weeks Female Mice 9

description: miRNA expression profiling was performed using the Nanostring nCounter® Mouse miRNA Assay kit v1.5 (Nanostring Technologies).

tag: tissue

value: 24 weeks


title: Tannerella forsythia infected 16 weeks Female Mice 10

value: 25 weeks


title: imb_koenig_2018_01_sub16, in vitro transcript library, 50nM U2AF2, rep2


title: Tannerella forsythia infected 16 weeks Male Mice 4

value: male

value: 19 weeks


title: Tannerella forsythia infected 16 weeks female mice 6

value: 21 weeks


title: Tannerella forsythia infected 16 weeks Male Mice 2

value: 17 weeks


title: Tannerella forsythia infected 16 weeks Male Mice 3

value: 18 weeks


title: Tannerella forsythia infected 8 weeks female Mice 9

source_name: Left Mandibles

tag: treatmen

value: 8 weeks


title: Tannerella forsythia infected 8 weeks female Mice 10


title: Tannerella forsythia infected 16 weeks Male Mice 5

value: 20 weeks


title: Tannerella forsythia infected 8 weeks female Mice 6


title: Tannerella forsythia infected 8 weeks male Mice 5


title: Tannerella forsythia infected 8 weeks female Mice 8


title: Tannerella forsythia infected 16 weeks Male Mice 1

value: 16 weeks


title: Tannerella forsythia infected 8 weeks male Mice 3


title: Tannerella forsythia infected 16 weeks Female Mice 7

value: 22 weeks


title: Tannerella forsythia infected 8 weeks male Mice 4


title: SHAM 16 weeks female Mice 8

value: sham


title: SHAM 16 weeks female Mice 7


title: SHAM 16 weeks female Mice 9


title: SHAM 16 weeks male Mice 5


title: SHAM 16 weeks female Mice 10


title: SHAM 16 weeks male Mice 4


title: Tannerella forsythia infected 8 weeks male Mice 2


title: SHAM 16 weeks Female mice 6


title: Tannerella forsythia infected 8 weeks male Mice 1


title: SHAM 8 weeks female Mice 10


title: SHAM 16 weeks male Mice 3


title: SHAM 16 weeks male Mice 2


title: SHAM 8 weeks female Mice 9


title: SHAM 16 weeks male Mice 1


title: Tannerella forsythia infected 8 weeks female Mice 7


title: SHAM 8 weeks female Mice 8

value: 15 weeks


title: SHAM 8 weeks female Mice 7

value: 14 weeks


title: SHAM 8 weeks male Mice 2

value: Left Mandibles

value: 9 weeks


title: SHAM 8 weeks male Mice 1


title: oocyte from antral follicle stage 5, gilt 803, rep4 [BS-Seq]

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Adaptors and low-quality reads/bases were first removed from raw FASTQ files by Trim Galore (v0.6.7) with parameters --stringency 3 --clip_R1 9 --clip_R2 9 --length 20.
Clean reads were aligned to the reference genome Sscrofa11.1 from Ensembl with the aligner BS-Seeker2 (v2.1.8) which invokes Bowtie 2.
The alignments results (bam files) of end-to-end and local modes were then merged. CGmapTools (v0.1.2) was used to generate and manipulate CGmap files which record the read counts mapped to each cytosine site.
Assembly: Sscrofa 11.1
Supplementary files format and content: the CG methylation calling results by Cgmaptools for each Sample

organism: Sus scrofa

source_name: ovary

growth_protocol: 208-210-day-old pubertal Landrace  Yorkshire pigs that were grown up in natural envrionment

extract_protocol:
Firstly, single oocyte in cell lysis buffer was vortexed for 2 min then centrifugated at 1200 g for 10 min at 4 ℃, resulting in the physical separation of mRNA and genomic DNA. The sediment containing nuclei was subjected to single-cell bisulfite scWGBS library construction.
Bisulfite conversion was carried out using EZ Methylation Direct bisulfite reagent (Zymo) on purified DNA in the presence of AMPure XP beads. BS-converted DNA was then submitted to preamplification using primers contained a 3’-random nonamers, and adaptors were incorporated during a total of five times of random priming and extension.  An extra 0.8 x AMPure XP purification was performed before final PCR amplification, then the purified libraries were ready for quality control and sequencing.

treatment_protocol: pigs were intraperitoneally injected with 5 IU of pregnant mare serum gonadotropin (PMSG) (Sigma Corporation, Guangdong, China) to stimulate antral follicular development. After 48 h, ovaries were dissected from gilts at a local slaughterhouse and transported to the laboratory within 2 hours in iced 0.1% DEPC PBS

value: ovary

value: oocyte

value: WT


title: H05_3

first: Sellers

last: Lab

address: 415 Main St

institute: Broad Institute

data_processing:
Standard PRISM data processing pipeline is described here https://github.com/cmap/dockerized_mts/blob/master/info/PRISM%20MTS%20data%20processing.pdf
Assembly: Alignment with known set of short barcode sequences
Supplementary files format and content: csv, barcode read counts for each cell line at each time point

source_name: PRISM (a mixture of 488 barcoded cancer cell lines)

extract_protocol:
11 days after transduction, cells were lysed in DNA lysis buffer (20mM Tris-HCl (pH 8.4), 50mM KCl, 0.45% NP40, 0.45% Tween-20, 10% Proteinase K) at 60°C for 1 hour. Samples lysed in DNA lysis buffer were denatured at 95º and amplified with a KAPA polymerase master mix (Roche, KK2602) PCR was performed in technical duplicates for each sample.
Indexed primers containing Illumina flow-cell sequences were obtained from IDT (forward: 5’AATGATACGGCGACCACCGAGATCTACANNNNNNNNAAGGTGCTTCTCGATC
TGCAT; reverse:5’CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCT where N represents the index nucleotides). Resulting products were confirmed to give single-band products of the expected size using gel electrophoresis and then pooled and purified for sequencing using the Zymo Select-a-Size DNA Clean & Concentrator kit (D4080). After pooling, the PCR product was quantified using the Qubit 3 Fluorometer. Samples were sequenced using Illumina HiSeq 2500 Rapid Run technology. Briefly, samples were loaded onto the flow cell at a final concentration of 10pM with a 20% PhiX spike-in due to low sequence diversity. Sequencing was run for 50 cycles with single-read setting. Raw sequencing reads in fastQ format were first processed to generate a table of cell-line barcode counts for each well, and barcode counts were then filtered for in-set cell lines.

tag: replicate

tag: time

value: p53 ORF


title: oocyte from antral follicle stage 5, gilt 803, rep3 [BS-Seq]


title: oocyte from antral follicle stage 5, gilt 803, rep1 [BS-Seq]


title: oocyte from antral follicle stage 5, gilt 205, rep1 [BS-Seq]


title: H06_3

tag: cell line

value: PRISM (a mixture of 488 barcoded cancer cell lines)

tag: treatment


title: oocyte from antral follicle stage 5, gilt 803, rep2 [BS-Seq]

tag: cell type

tag: genotype


title: oocyte from antral follicle stage 5, gilt 205, rep2 [BS-Seq]


title: H03_3

value: GFP ORF


title: SHAM 8 weeks male Mice 3

value: 10 weeks


title: oocyte from antral follicle stage 5, gilt 201, rep2 [BS-Seq]


title: SHAM 8 weeks male Mice 4

value: 11 weeks


title: oocyte from antral follicle stage 4, gilt 803, rep2 [BS-Seq]


title: oocyte from antral follicle stage 4, gilt 803, rep1 [BS-Seq]


title: oocyte from antral follicle stage 4, gilt 803, rep3 [BS-Seq]


title: oocyte from antral follicle stage 4, gilt 801, rep4 [BS-Seq]


title: oocyte from antral follicle stage 4, gilt 801, rep3 [BS-Seq]


title: oocyte from antral follicle stage 4, gilt 801, rep1 [BS-Seq]


title: H04_3


title: oocyte from antral follicle stage 4, gilt 801, rep2 [BS-Seq]


title: H02_3


title: oocyte from antral follicle stage 5, gilt 803, rep5 [BS-Seq]


title: H01_3


title: SHAM 8 weeks male Mice 5

value: 12 weeks


title: SHAM 8 weeks female Mice 6

value: 13 weeks


title: oocyte from antral follicle stage 5, gilt 201, rep1 [BS-Seq]


title: oocyte from antral follicle stage 5, gilt 201, rep3 [BS-Seq]


title: oocyte from antral follicle stage 4, gilt 205, rep2 [BS-Seq]


title: G12_3

value: KRASG12V ORF


title: G11_3


title: oocyte from antral follicle stage 4, gilt 205, rep1 [BS-Seq]


title: G10_3


title: oocyte from antral follicle stage 4, gilt 201, rep1 [BS-Seq]


title: oocyte from antral follicle stage 3, gilt 803, rep4 [BS-Seq]


title: oocyte from antral follicle stage 3, gilt 803, rep3 [BS-Seq]


title: oocyte from antral follicle stage 3, gilt 803, rep2 [BS-Seq]


title: oocyte from antral follicle stage 3, gilt 801, rep1 [BS-Seq]


title: oocyte from antral follicle stage 3, gilt 201, rep2 [BS-Seq]


title: oocyte from antral follicle stage 3, gilt 205, rep1 [BS-Seq]


title: oocyte from antral follicle stage 2, gilt 803, rep2 [BS-Seq]


title: oocyte from antral follicle stage 3, gilt 201, rep3 [BS-Seq]


title: F07_3

value: CTNNB1 ORF


title: oocyte from antral follicle stage 3, gilt 201, rep1 [BS-Seq]


title: G05_3

value: CDKN2A ORF


title: F09_3


title: oocyte from antral follicle stage 2, gilt 803, rep1 [BS-Seq]


title: F06_3

value: AKTE17K ORF


title: F08_3


title: F04_3


title: F05_3


title: G06_3


title: G01_3

value: PTEN ORF


title: G02_3


title: G03_3


title: G04_3


title: oocyte from antral follicle stage 3, gilt 205, rep2 [BS-Seq]


title: oocyte from antral follicle stage 2, gilt 801, rep3 [BS-Seq]


title: oocyte from antral follicle stage 2, gilt 801, rep2 [BS-Seq]


title: oocyte from antral follicle stage 3, gilt 803, rep1 [BS-Seq]


title: cell_I18_S79

description: NextSeq Mid 2 X 75 per flow

tag: strain

value: CD1 mice, strain  #022 from Charles River

value: somatosensory neuron

tag: classification

value: glabrous

value: I


title: E11_3

value: ERK2 ORF


title: oocyte from antral follicle stage 2, gilt 801, rep1 [BS-Seq]

value: ovary

value: oocyte

value: WT


title: E10_3

value: PRISM (a mixture of 488 barcoded cancer cell lines)


title: oocyte from antral follicle stage 2, gilt 205, rep1 [BS-Seq]


title: E09_3

value: EGFRexon10del ORF


title: E12_3


title: oocyte from antral follicle stage 2, gilt 201, rep4 [BS-Seq]


title: E07_3


title: E08_3


title: oocyte from antral follicle stage 2, gilt 201, rep3 [BS-Seq]


title: E05_3

value: MED1DD ORF


title: oocyte from antral follicle stage 1, gilt 801, rep2 [BS-Seq]


title: oocyte from antral follicle stage 2, gilt 201, rep1 [BS-Seq]


title: oocyte from antral follicle stage 2, gilt 201, rep2 [BS-Seq]


title: oocyte from antral follicle stage 1, gilt 803, rep1 [BS-Seq]


title: E03_3

value: BRAFV600E ORF


title: E02_3


title: D06_3

value: p53 ORF


title: E01_3


title: E06_3


title: oocyte from antral follicle stage 1, gilt 801, rep1 [BS-Seq]


title: E04_3


title: D03_3

value: GFP ORF


title: D05_3


title: D04_3


title: oocyte from antral follicle stage 1, gilt 201, rep3 [BS-Seq]


title: oocyte from antral follicle stage 1, gilt 201, rep1 [BS-Seq]


title: oocyte from antral follicle stage 1, gilt 201, rep4 [BS-Seq]


title: oocyte from antral follicle stage 1, gilt 201, rep2 [BS-Seq]


title: oocyte from antral follicle stage 1, gilt 803, rep2 [BS-Seq]


title: oocyte from antral follicle stage 1, gilt 803, rep3 [BS-Seq]


title: oocyte from antral follicle stage 1, gilt 205, rep1 [BS-Seq]


title: D01_3


title: C12_3

value: KRASG12V ORF


title: oocyte from antral follicle stage 5, gilt 803, rep3

data_processing:
Raw sequencing reads were trimmed to remove low-quality reads and adaptors by TrimGalore (v0.4.3)
Hisat2 (v2.1.0) was used to align reads to the reference genome
A count matrix was generated using featureCounts with the Ensembl gene annotation (v93)
A TPM matrix was generated using STRINGTIE(v1.2.2) with the Ensembl gene annotation (v94)
Assembly: Sscrofa 11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM for each Sample

extract_protocol:
Firstly, single oocyte in cell lysis buffer was vortexed for 2 min then centrifugated at 1200 g for 10 min at 4 ℃, resulting in the physical separation of mRNA and genomic DNA. The supernatant containing cytoplasm transcriptome was subjected to Smart-seq2 protocol for single-cell full-length cDNA library construction
Briefly, the full-length cDNA synthesis was performed by addition of template switch oligo and SuperScript II reverse transcriptase (Invitrogen) to the 4 μL of supernatant and incubated at 42 ℃ for 90 min following by 10 cycles of 50 ℃ 2 min and 42℃ for 2 min. The reverse transcriptase was inactivated at 70 ℃ for 15 min. The single stranded cDNA was subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at 1 x concentration for 16 cycles. The amplified cDNA was purified using AMpure XP beads (Beckman) and then used for library construction using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). Smart-seq2


title: oocyte from antral follicle stage 5, gilt 803, rep4


title: C10_3


title: oocyte from antral follicle stage 5, gilt 803, rep2


title: D02_3


title: C11_3


title: C06_3

value: CDKN2A ORF


title: oocyte from antral follicle stage 5, gilt 205, rep3


title: C05_3


title: oocyte from antral follicle stage 5, gilt 201, rep3


title: C02_3

value: PTEN ORF


title: C01_3


title: C03_3


title: C04_3


title: oocyte from antral follicle stage 5, gilt 205, rep1


title: oocyte from antral follicle stage 5, gilt 201, rep2


title: oocyte from antral follicle stage 5, gilt 201, rep1


title: oocyte from antral follicle stage 4, gilt 803, rep4


title: B09_3

value: CTNNB1 ORF


title: oocyte from antral follicle stage 4, gilt 803, rep1


title: B07_3


title: oocyte from antral follicle stage 4, gilt 803, rep2


title: B05_3

value: AKTE17K ORF


title: B08_3


title: oocyte from antral follicle stage 4, gilt 803, rep3


title: B06_3


title: oocyte from antral follicle stage 5, gilt 803, rep1


title: B04_3


title: oocyte from antral follicle stage 4, gilt 801, rep3


title: oocyte from antral follicle stage 4, gilt 801, rep2


title: A11_3


title: oocyte from antral follicle stage 4, gilt 801, rep1


title: oocyte from antral follicle stage 5, gilt 205, rep2


title: A10_3


title: A09_3


title: A12_3


title: oocyte from antral follicle stage 4, gilt 205, rep2


title: oocyte from antral follicle stage 4, gilt 201, rep1


title: A08_3


title: A07_3


title: oocyte from antral follicle stage 3, gilt 803, rep4


title: oocyte from antral follicle stage 3, gilt 803, rep3


title: A06_3


title: A04_3


title: oocyte from antral follicle stage 3, gilt 803, rep2


title: oocyte from antral follicle stage 3, gilt 803, rep1


title: oocyte from antral follicle stage 4, gilt 801, rep4


title: A05_3


title: A02_3


title: oocyte from antral follicle stage 3, gilt 801, rep1


title: oocyte from antral follicle stage 3, gilt 205, rep1


title: A03_3


title: A01_3


title: oocyte from antral follicle stage 3, gilt 205, rep2


title: oocyte from antral follicle stage 3, gilt 201, rep4


title: oocyte from antral follicle stage 3, gilt 201, rep3


title: oocyte from antral follicle stage 4, gilt 205, rep1


title: oocyte from antral follicle stage 3, gilt 201, rep2


title: oocyte from antral follicle stage 3, gilt 201, rep1


title: oocyte from antral follicle stage 2, gilt 803, rep3


title: oocyte from antral follicle stage 2, gilt 803, rep4


title: oocyte from antral follicle stage 2, gilt 803, rep1


title: oocyte from antral follicle stage 2, gilt 803, rep2


title: oocyte from antral follicle stage 2, gilt 801, rep3


title: Adjacent 4

city: Ningbo

first: Xianjiang

last: Wu

state: None Selected

address: No.41 Xibei Street

institute: Ningbo No.2 Hospital

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences.
In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered.
Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Thyroid

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (NovaSeq 6000) and 150 bp/125bp paired-end reads were generated.

value: Thyroid


title: PTC 4


title: Adjacent 2


title: PTC 3


title: Adjacent 3


title: PTC 1


title: oocyte from antral follicle stage 2, gilt 801, rep4


title: Adjacent 1


title: oocyte from antral follicle stage 2, gilt 801, rep1


title: oocyte from antral follicle stage 2, gilt 801, rep2


title: oocyte from antral follicle stage 2, gilt 205, rep1


title: oocyte from antral follicle stage 2, gilt 201, rep3


title: oocyte from antral follicle stage 2, gilt 201, rep1


title: DEN1037A_Day0_Shot1_run1_PBMC

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed reads were aligned to the GRCh38 reference genome (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1a
RseQC was used to assess strand specificity for all transcripts
HTSeq was used to estimate transcript abundance from unique mapped reads
Raw reads were normalized using DESeq2 v1.26.0
Assembly: GRCh38
Supplementary files format and content: counts

source_name: PBMC

extract_protocol:
RNEasy micro-kit (QIAGEN)
TruSeq Stranded Total RNA Library Prep kit after rRNA and globin mRNA removal using the Globin-Zero Gold rRNA removal kit.

tag: batch

tag: timepoint

tag: immunization

tag: participant

tag: breadth

value: high

tag: serostatus before immunization

value: Seronegative


title: DEN1049A_Day0_Shot1_run1_PBMC

value: low


title: DEN1030A_Day0_Shot1_run1_PBMC


title: DEN1042A_Day0_Shot1_run1_PBMC


title: DEN1044A_Day0_Shot1_run1_PBMC


title: DEN1021A_Day0_Shot1_run1_PBMC


title: DEN1047A_Day0_Shot1_run1_PBMC


title: oocyte from antral follicle stage 1, gilt 803, rep4

value: ovary

value: oocyte


title: oocyte from antral follicle stage 2, gilt 201, rep2

value: WT


title: PTC 2


title: DEN1017A_Day0_Shot1_run1_PBMC


title: DEN1016A_Day0_Shot1_run1_PBMC


title: DEN1034A_Day0_Shot1_run1_PBMC


title: DEN1010A_Day0_Shot1_run1_PBMC


title: DEN1009A_Day0_Shot1_run1_PBMC


title: DEN1004A_Day0_Shot1_run1_PBMC


title: oocyte from antral follicle stage 1, gilt 803, rep1


title: DEN1001A_Day0_Shot1_run1_PBMC


title: DEN1049A_Day0_Shot1_run2_PBMC


title: oocyte from antral follicle stage 1, gilt 801, rep2


title: DEN1050A_Day0_Shot1_run2_PBMC


title: oocyte from antral follicle stage 1, gilt 801, rep3


title: DEN1043A_Day0_Shot1_run2_PBMC


title: DEN1045A_Day0_Shot1_run2_PBMC


title: oocyte from antral follicle stage 1, gilt 205, rep1


title: oocyte from antral follicle stage 1, gilt 201, rep2


title: DEN1038A_Day0_Shot1_run2_PBMC


title: oocyte from antral follicle stage 1, gilt 803, rep3


title: oocyte from antral follicle stage 1, gilt 201, rep1


title: DEN1036A_Day0_Shot1_run2_PBMC


title: DEN1035A_Day0_Shot1_run2_PBMC


title: DEN1027A_Day0_Shot1_run2_PBMC


title: PRO-seq_20h_Biorep2.1 (reanalyzed)

description:
Re-analysis of Sample  GSM4873701 to new Sp 5.0 version of the genome.
20h_5.0_minus3.rpm.bw
20h_5.0_plus3.rpm.bw
20h_5.0_3_.dREG.peak.prob_100_merged_sort.bed

source_name: 8 hour hatching blastula embryos

value: 8 hour hatching blastula embryos

value: Wild


title: PRO-seq_20h_Biorep4 (reanalyzed)

description:
Re-analysis of Sample GSM4873704 to new Sp 5.0 version of the genome.
20h_5.0_minus3.rpm.bw
20h_5.0_plus3.rpm.bw
20h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: PRO-seq_20h_Biorep2.2 (reanalyzed)

description:
Re-analysis of Sample GSM4873702 to new Sp 5.0 version of the genome.
20h_5.0_minus3.rpm.bw
20h_5.0_plus3.rpm.bw
20h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: oocyte from antral follicle stage 1, gilt 801, rep1


title: DEN1033A_Day0_Shot1_run2_PBMC


title: DEN1029A_Day0_Shot1_run2_PBMC


title: PRO-seq_12h_Biorep3 (reanalyzed)

description:
Re-analysis of Sample GSM4988036 to new Sp 5.0 version of the genome.
12h_5.0_minus3.rpm.bw
12h_5.0_plus3.rpm.bw
12h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: DEN1025A_Day0_Shot1_run2_PBMC


title: DEN1023A_Day0_Shot1_run2_PBMC


title: oocyte from antral follicle stage 1, gilt 201, rep3


title: DEN1021A_Day0_Shot1_run2_PBMC


title: DRG, Neat1 shRNA AAV vector + SNL, Day14, rep3

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

institute: Nippon Medical School

data_processing:
The reads were aligned to the Rattus norvegicus USCS rn5 reference genome with RefSeq gene annotation and were constructed into transcripts using RNA-Seq Alignment v1.0
FPKM values were calculated by Cufflinks Assembly & DE v2.0.
Assembly: rn5
Supplementary files format and content: FPKM values

organism: Rattus norvegicus

source_name: DRG

extract_protocol:
Total RNA was extracted using RNAiso plus (Takara Bio, Shiga, Japan).
A polyadenylated RNA library was prepared using a TruSeq stranded mRNA LT sample Prep Kit (Illumina, San Diego, CA).

value: DRG

value: Sprague Dawley

tag: Sex

value: male

value: shRNA AAV vector + SNL

value: Day 14 after SNL


title: DRG, Neat1 shRNA AAV vector + SNL, Day14, rep2

tag: tissue


title: FFGR4

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

data_processing:
data quality was validated for RNAseq analysis using FastQC Version 0.11.9.
aligned with the sequencing data using Salmon
Integrated differential expression and pathway analysis were conducted with iDep.96 web-based applications
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: txt file format - contains TPM

source_name: Perirenal Adipose Tissue

extract_protocol:
adipose tissue was thawed in Trizol and homogenized using 3 pulses, 4-6 seconds each. Then, 0.2 mL of chloroform was added per 1 mL of Trizol (0.1 mL per sample). Samples were centrifuged for 15 minutes at 14,000 x g (4 ˚C) and the mixture separated into a lower red phenol-chloroform, interphase, and a colorless upper aqueous solution. The aqueous phase containing RNA was transferred to a new tube very carefully to ensure proteins and other cell components did not contaminate the RNA. Then, 250 µl of isopropanol was added to the aqueous phase (0.5 ml/ ml of Trizol) and incubated for 10 minutes. The sample was centrifuged for 10 minutes at 14,000 x g (4˚C) and the RNA precipitate formed a white gel-like pellet at the bottom of the tube. The supernatant was discarded and the sample was vortexed briefly before centrifugation for 5 minutes at 8000 x g (4˚C). The supernatant was discarded and the RNA pellet was air-dried for 10 minutes. Pellets were resuspended in 50 µl of RNase-free water. The RNA was further purified by Zymo Purelink RNA columns.
library was constructed from samples using a Swift RNA Library Kit – (Catalog # R1024) and Swift Dual Combinatorial Indexing Kit – (Catalog # X8096)

value: Perirenal Adipose Tissue

value: Female

value: Hyperthermia


title: PRO-seq_12h_Biorep1.2 (reanalyzed)

description:
Re-analysis of Sample GSM4988034  to new Sp 5.0 version of the genome.
12h_5.0_minus3.rpm.bw
12h_5.0_plus3.rpm.bw
12h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: DRG, Neat1 shRNA AAV vector + SNL, Day14, rep1


title: PRO-seq_12h_Biorep2 (reanalyzed)

description:
Re-analysis of Sample GSM4988035  to new Sp 5.0 version of the genome.
12h_5.0_minus3.rpm.bw
12h_5.0_plus3.rpm.bw
12h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: DEN1034A_Day0_Shot1_run2_PBMC


title: FFGR3


title: PRO-seq_12h_Biorep1.1 (reanalyzed)

description:
Re-analysis of Sample GSM4988033 to new Sp 5.0 version of the genome.
12h_5.0_minus3.rpm.bw
12h_5.0_plus3.rpm.bw
12h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: FFGR2


title: PRO-seq_20h_Biorep1 (reanalyzed)

description:
Re-analysis of Sample  GSM4873700 to new Sp 5.0 version of the genome.
20h_5.0_minus3.rpm.bw
20h_5.0_plus3.rpm.bw
20h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: DEN1018A_Day0_Shot1_run2_PBMC


title: DEN1014A_Day0_Shot1_run2_PBMC


title: ATAC_12h_Bioreplicate 2 (reanalyzed)

description:
Re-analysis of Sample GSM4988038 to new Sp 5.0 version of the genome. It should be included in SubSeries GSE234139
ATAC_12h6_ATAC12h7_RPM.bw
12h_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed

data_processing:
ENCOCE-DCC atac-seq-pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) default parameters
MACS2 peak call p threshold set to 0.05.
Assembly: Sp5.0

source_name: 12 hour embryos

extract_protocol:
Density gradient nuclear prep was used for all samples (Arenas-Mena et. al, 2021) https://doi.org/10.1186/s12864-021-07936-0, except for the 72h and Red Spherule cell samples, for which the Omni-ATAC protocol (Corces et al., 2017) was ussed,  as indicated.
ATAC-seq (Arenas-Mena et. al, 2021) https://doi.org/10.1186/s12864-021-07936-0

value: 12 hour embryos


title: PRO-seq_20h_Biorep3 (reanalyzed)

description:
Re-analysis of Sample GSM4873703 to new Sp 5.0 version of the genome.
20h_5.0_minus3.rpm.bw
20h_5.0_plus3.rpm.bw
20h_5.0_3_.dREG.peak.prob_100_merged_sort.bed


title: DRG, control AAV vector + SNL, Day14, rep2

value: control AAV vector + SNL


title: FC4

value: Control


title: FFGR1


title: xenograft-6R_2

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

description:
RAB27A KD Technical replicate 4
human-VJ-3468-6R_S10.featurecounts.txt
mouse-VJ-3468-6R_S10.featurecounts.txt

data_processing:
Trimming with fastp
Alignment with hista2
deconvolution of mouse and human reads in xenograft sequence data with XenofilteR
Assembly: Homo_sapiens.GRCh38 & Mus_musculus.GRCm39
Supplementary files format and content: tab-delimited text files include quantified reads from FeatureCounts

organism:
Homo sapiens
Mus musculus

source_name: xenograft formed by subcutaneously injected human cSCC cells (UT-SCC-7) and infiltrating mouse stroma cells

growth_protocol: UT-SCC-7 cells were cultured in DMEM with 10% FBS, 1% HEPES, 1% NEA and 1% P+S in vitro, and subcutaneously injected into NOD SCID gamma (NSG) mice for xenograft experiments. Cell suspension in 100 µl of ice-cold medium was mixed at 1:1 volume ratio with Matrigel right before the injection.

extract_protocol:
RNA was extracted using miRNeasy Mini Kit  (QIAGEN).
Library preparation was constructed using the TruSeq stranded mRNA library preparation kit with polyA selection (Illumina Inc.) according to the manufacturer’s instructions

treatment_protocol: Stable RAB27A knockdown and control UT-SCC-7 cell lines were established by lentiviral transduction with TurboRFP as a selection marker (GeneCopoeia). The transduced cells were selected based on the expression of RFP within the cells using fluorescent-activated cell sorter (FACS).

value: RAB27A knockdown

value: shRAB27A lentiviral transduction