title: ChIPseq-SET14-H3K27me3-EYFP-ZF-rep2

description: ChIP-seq data set14 of H3K27me3-EYFP-ZF repliate2

extract_protocol: ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).

value: leaf tissue

value: anti-H3K27me3 (Millipore Sigma)


title: ChIPseq-SET15-H3K9ac-fwa-rep1

status: Public on Jan 20 2023

type: SRA

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

description: ChIP-seq data set15 of H3K9ac-fwa repliate1

library_source: genomic

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
BS-sPCR reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Assembly: tair10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Leaf tissues were collected from 4-5 week plants

tag: tissue

tag: developmental stage

value: 4-5 weeks

tag: strain

tag: antibody

value: anti-H3K9ac (Abcam)

tag: target protein


title: 2B: Visceral nociceptors AAI 1

city: Montréal

first: Theo

last: Crosson

state: Quebec

address: 2900 Boulevard Edouard Montpetit

country: Canada

institute: Université de Montréal

library_source: transcriptomic

data_processing:
Demultiplexing
trimming for sequencing adapters and low quality 3' bases
Alignement to GRCm38 with STAR version 2.7.1
FPKM calculation
Assembly: GRCm38
Supplementary files format and content: STAR readcount
Supplementary files format and content: FPKM

molecule: total RNA

organism: Mus musculus

source_name: Jugular-nodose complex (JNC)

extract_protocol:
RNA was separated from protein and DNA by mixing 500μL sample in Trizol with 100μL chloroform before ultracentrifugation (15min, 16000g, 4°). The upperphase was mixed with a half volume of 100° isopropanol, transferred to a purification column, and the RNA purified using the kit PureLink™ RNA Micro Scale (Thermofisher #12183016) following manufacturer’s instructions.
KAPA mRNA HyperPrep Kit (KapaBiosystems #KR1352)
Capture mRNA with oligo-dT bead, RT with random priming, second strand synthesis with dUTP, adapter ligation and strand specific library amplification

value: Jugular-nodose complex (JNC)

tag: cell type

value: Visceral Nociceptors (Nav1.8+DID-)

tag: genotype

tag: treatment

value: AAI


title: ChIPseq-SET14-H3-EYFP-ZF-rep2

description: ChIP-seq data set14 of H3-EYFP-ZF repliate2

value: anti-H3 (Abcam)


title: priB_TriC_B18AIDKO_Emucapture_+3hTPL_rep3

city: Vienna

first: Maximilian

middle: Christian

last: von der Linde

state: Vienna

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

country: Austria

institute: Institute of Molecular Pathology

description: Tri-C

data_processing:
Tri-C
Demulitplexed reads were submitted to the CCseqBasicS5 pipeline with following options: bowtie2 alignment to NCBI mm9 , --tric, --flashbases 10
matrices were generated using the modified TriC_matrix_simple_MO.py script
Reads with alt least three interactions were extracted with TriCgetreads.py
Visualisation with pyplot in TriCplot.py
Find more information and scripts at https://github.com/PavriLab/tric
Assembly: mm9
Supplementary files format and content: Tab separated matrix showing normalized interaction counts
Library strategy: Tri-C

source_name: primary B-cells

growth_protocol: Complete RPMI medium with LPS and IL4 for activation

extract_protocol:
TriC was performed as described (Downes et al 2022 with modifications desribed in Costea, Schoeberl et al 2022). In short, 10x10^6 or 15x10^6 (0h) cells were crosslinked with 2% HCHO for 8 min at room temperature. After quenching with 0,133M glycine, cells were lysed and nuclei isolated. Next, nuclei were lysed followed by NlaIII digestion (overnight), T4-DNA-ligation (overnight), Proteinase K digestion (overnight) and genomic DNA extraction. DNA was sonicated on Covaris S2 sonicator.
TriC library was prepared of 3x2µg sonicated DNA using NEBUltraII and barcoding PCRs were performed using Nextflex unique dual index barcode sequences. For capture using reagents of the Roche HyperCap target enrichment kit and mouse Cot-1, 1-2µg of libraries were 2x (72h, 24h) hybridized to 2.9nM of individual biotinylated capture probes, followed by streptavidin pull down and PCR amplification using P5 and P7 (Illumina) primer sequences. Samples were multiplexed for sequencing on NextSeq or NovaSeq (Illumina) platforms

tag: capture probe

value: Emu capture

value: 72h activated, 3h TPL treated

tag: clone

value: clone 1

tag: replicate

value: replicate 3


title: 3B: Visceral nociceptors naive 2

value: Naive


title: priB_TriC_B18AIDKO_Emucapture_+3hTPL_rep1

description: Tri-C

value: replicate 1


title: 5A: Airway nociceptors naive 3

value: Airway Nociceptors (Nav1.8+DID+)


title: 2A: Airway nociceptors AAI 1


title: iWAT pAd GFP 1

city: Boston

first: Melanie

middle: J

last: Mittenbühler

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

data_processing:
Raw reads were mapped or aligned to the reference organism using STAR software
Differential gene expression testing was performed by DESeq and resulting fold change values were used as a pre-ranked gene list for gene set enrichment analysis.
For DESeq analysis data are expressed as (PSAP pAd/GFP pAd).
Assembly: mm10
Supplementary files format and content: STAR Gene counts TPM and a list of differentially-expressed genes deseq

source_name: primary iWAT cells

growth_protocol: Inguinal white adipose stromal-vascular fraction (SVF) was isolated and cultured as described previously (Seale et al., 2011). For experiments, cells were grown until confluency. Afterwards, differentiation of pre-adipocytes was induced by treatment with an adipogenic cocktail (1 μM rosiglitazone (Cayman Chemical, 71740), 0.5 mM 3-Isobutyl-1-methylxanthine (IBMX) (Sigma Aldrich, I5879), 1 μM dexamethasone (Sigma Aldrich, D4902), 870 nM insulin (Sigma Aldrich, I5500)) in complete adipocyte culture medium for 2 days. Subsequently, medium was changed to complete adipocyte maintenance medium containing 1 μM rosiglitazone and 870 nM insulin.

extract_protocol:
cells were harvested and flash frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent and RNeasy column (QIAGEN).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7

treatment_protocol: Adenoviral transduction was performed at day 3-4 post differentiation initiation at an multiplicity of infection (MOI) of 100 per cell. Medium was changed 24 h afterwards and cells were harvested 72 h post transduction.

value: primary iWAT cells

value: WT

value: pAd GFP

tag: time

value: 3 days


title: ChIPseq-SET14-H3K27me3-EYFP-ZF-rep1

description: ChIP-seq data set14 of H3K27me3-EYFP-ZF repliate1

value: leaf tissue

value: 4-5 weeks

value: anti-H3K27me3 (Millipore Sigma)


title: iWAT pAd GFP 2


title: 6A: Airway nociceptors AAI 3

value: Jugular-nodose complex (JNC)


title: priB_TriC_B18AIDKO_Emucapture_+1hTPL_rep2

description: Tri-C

value: 72h activated, 1h TPL treated

value: replicate 2


title: RPE, Itgb5-/-, P25, Biol rep 1 [Itgb5_1]

city: New Haven

first: Maria

middle: Elisa

last: Mercau

address: 300 Cedar st

department: Immunobiology

institute: Yale University

data_processing:
Raw reads were subjected to trimming by btrim to remove sequencing adaptors and low-quality regions.
Reads were mapped to the mouse genome (GRCm38) using STAR
After counts are collected, Deseq2 package was run to identify differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files which include normalized counts for each sample

molecule: polyA RNA

source_name: retinal pigment epithelium (RPE)

extract_protocol:
RNA from RPE cells was extracted using Rneasy Mini kit (Qiagen) following manufacturer’s instructions.
Libraries were prepared following the illumina paired-end sequencing protocol as detailed here (https://medicine.yale.edu/keck/ycga/sequencing/illumina/1_21591_284_12501_v1.pdf)

value: retinal pigment epithelium (RPE)

value: epithelial

value: none, direct ex-vivo use


title: RPE, WT129, P25, Biol rep 1 [WT129_1]


title: iWAT pAd PSAP 3

value: pAd PSAP


title: Lemd2 p.L13R KI, #33/4237, 9 months old [Lemd2_33_4237_KI_9m]

city: Würzburg

first: Ruping

last: Chen

state: Bavaria

address: Am Schwarzenberg 15

department: Comprehensive Heart Failure Center

country: Germany

institute: University hospital Würzburg

description: KI 4

data_processing:
Sequencing was performed at 25 million reads/sample with 75 nt read length on the NextSeq 500 platform (Illumina)
Illumina reads were quality- and adapter-trimmed via Cutadapt version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded
Processed reads were subsequently mapped to the mouse genome (GRCm38.p6) using STAR v2.7.2b with default parameters.
Read count were generated using featureCounts v1.6.4 from the Subread package
Assembly: GRCm38.p6
Supplementary files format and content: excel file including raw counts of each gene for each sample

source_name: heart

growth_protocol: Mice were housed in a climate-controlled facility with a 12-hour light/dark cycle, and provided access to standard mouse chow and water ad libitum

extract_protocol:
RNA was harvested using RNA extraction kit (Qiagen). 0.5µl of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions

treatment_protocol:
None
None

value: heart

value: Lemd2 p.L13R knock-in

tag: age

value: 9 months old


title: 3A: Airway nociceptors naive 2

value: Airway Nociceptors (Nav1.8+DID+)

value: Naive


title: RPE, Tyro3-/-V1, P25, Biol rep 3 [Tyro3_23_3]


title: iWAT pAd GFP 4

value: primary iWAT cells

value: WT

value: pAd GFP


title: iWAT pAd PSAP 4

value: 3 days


title: Lemd2 p.L13R KI, #23+10/2552, 9 months old [Lemd2_23plus10_2552_old]

description: KI 2


title: priB_TriC_B18AIDKO_Emucapture_+1hTPL_rep1

description: Tri-C

value: Emu capture

value: clone 1

value: replicate 1


title: RPE, Tyro3-/-V1, P25, Biol rep 2 [Tyro3_23_2]


title: ChIPseq-SET14-H3-fwa-rep1

description: ChIP-seq data set14 of H3-fwa repliate1

value: leaf tissue

value: 4-5 weeks

value: anti-H3 (Abcam)


title: ChIPseq-SET13-PolII-Col-0-rep2

description: ChIP-seq data set13 of Pol II-Col-0 repliate2

value: anti-Pol II (Abcam)

value: Pol II


title: iWAT pAd GFP 3


title: Lemd2 p.L13R KI, #21+30/2550, 9 months old [Lemd2_21plus30_2550_KI]

description: KI 1

value: heart


title: RPE, C57BL/6, P25, Biol rep 6 [BL6J_9]

value: retinal pigment epithelium (RPE)

value: epithelial

value: none, direct ex-vivo use


title: RPE, Tyro3-/-V1, P25, Biol rep 1 [Tyro3_23_1]


title: RPE, C57BL/6, P25, Biol rep 4 [BL6J_7]


title: ChIPseq-SET12-H3-elf7-rep1

description: ChIP-seq data set12 of H3-elf7 repliate1


title: ChIPseq-SET14-H3-ELF7-ZF-rep1

description: ChIP-seq data set14 of H3-ELF7-ZF repliate1


title: RPE, C57BL/6, P25, Biol rep 3 [B6J_23_3]


title: RPE, C57BL/6, P25, Biol rep 5 [BL6J_8]


title: ChIPseq-SET13-PolII-elf7-rep2

description: ChIP-seq data set13 of Pol II-elf7 repliate2


title: RPE, Itgb5-/-, P25, Biol rep 3 [Itgb5_3]


title: ChIPseq-SET14-H3-EYFP-ZF-rep1

description: ChIP-seq data set14 of H3-EYFP-ZF repliate1


title: RPE, WT129, P25, Biol rep 3 [WT129_3]


title: ChIPseq-SET13-H3-Col-0-rep2

description: ChIP-seq data set13 of H3-Col-0 repliate2


title: 1A: Airway nociceptors naive 1

value: Jugular-nodose complex (JNC)

value: Airway Nociceptors (Nav1.8+DID+)

value: Naive


title: Lemd2 p.L13R KI, #34/4238, 9 months old [Lemd2_34_4238_KI_9m]

description: KI 5

value: Lemd2 p.L13R knock-in

value: 9 months old


title: ChIPseq-SET13-H3-elf7-rep2

description: ChIP-seq data set13 of H3-elf7 repliate2


title: RPE, Itgb5-/-, P25, Biol rep 2 [Itgb5_2]


title: RPE, WT129, P25, Biol rep 2 [WT129_2]


title: ChIPseq-SET12-PolII-elf7-rep1

description: ChIP-seq data set12 of Pol II-elf7 repliate1


title: Lemd2 p.L13R KI, #43/6610, 9 months old [Lemd2_43_6610_new]

description: KI 6


title: RPE,Mertk-/-V2Tyro3-/-V2, P25, Biol rep 2 [DKO_23_2]


title: WT, #57/7616, 9 months old [Lemd2_57_7616_WT]

description: WT 3

value: wild-type


title: KO1, H3K4, CD41pos

city: Cincinnati

first: Chen

last: Wang

state: OH

address: 3333 Burnet Avenue

department: Experimental Hematology/Oncology

institute: CCHMC

data_processing:
CUT&RUN-seq reads in FASTQ format were first subjected to quality control to assess  the need for trimming of adapter sequences or bad quality segments. The programs  used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2 and cutadapt v1.9.1.
The trimmed reads were aligned to the reference mouse genome version mm10  with the program BOWTIE v2.3.4.1.Peaks were called using the program MACS v2.1.0.
Common peaks among all samples were obtained by merging called peaks at 50% overlap  using BEDtools v2.27.0. This was done at two levels, between replicates and between  treatments. In the former, we require peaks to be present in one of the biological replicates,  On the latter, we merge at 50% all replicate peaks to define a set of common peaks to all data sets.
The common peaks, originally in BED format were converted to a Gene Transfer Format (GTF) to enable fast counting of reads under the peaks with the program featureCounts v1.6.2 (Rsubread package).Each feature in the GTF file has the value "peak" on the second column.
Peaks are annotated by nearest or overlapping gene and genomic features using in-house script.(Promoter : 1kb upstream and downstream from TSS,Upstream :  between 21 upstream and 1 kb upstream from TSS. Annotation priority : Promoter>Upstream>Exon>Intron )
Plots were generated using the ggplot2 (10) package and base graphics in R.
Assembly: mm10
Supplementary files format and content: Bigwig files containing trimed and aligned reads for each sample;matrix_annotate.feat files contain raw read counts for all samples in the according category;matrix_annotate.tpm  files contain Transcripts Per Million(TPM) counts for all samples in the according category.
Library strategy: CUT&RUN Chip-seq

source_name: bone marrow

extract_protocol:
Cells were sorted by FACS and processed following CUT&RUN protocol: https://www.cellsignal.com/learn-and-support/protocols/cut-and-run-protocol
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep with Sample Purification Beads.(E7103S)
primers were used as NEBNext® Multiplex Oligos for Illumina®

value: KO

value: bone marrow

value: CD41pos HSC

tag: chip antibody


title: WT, #71/7016, 9 months old [Lemd2_71_7016_WT]

description: WT 5


title: RPE, C57BL/6, P25, Biol rep 2 [B6J_23_2]


title: WT, #15/0485, 9 months old [Lemd2_15_0485_WT]

description: WT 1


title: RPE,Mertk-/-V2Tyro3-/-V2, P25, Biol rep 1 [DKO_23_1]


title: KO2, RUNX1, CD41pos

value: RUNX1 (donation from collaborator Dr. Wu)


title: ChIPseq-SET11-PolII-fwa-rep2

description: ChIP-seq data set11 of Pol II-fwa repliate2

value: leaf tissue

value: 4-5 weeks


title: WT2, H3K4, CD41neg

value: WT

value: CD41neg HSC


title: WT, #70/7629, 9 months old [Lemd2_70_7629_WT]

description: WT 4

value: heart


title: Lemd2 p.L13R KI, #32/4236, 9 months old [Lemd2_32_4236_KI_9m.fq.gz]

description: KI 3


title: ChIPseq-SET12-PolII-Col-0-rep1

description: ChIP-seq data set12 of Pol II-Col-0 repliate1

value: anti-Pol II (Abcam)

value: Pol II


title: Nlrx1 deficient BMDCs 12hrs post challenge Replicate 3

city: Blacksburg

first: Shiv

middle: D.

last: Kale

state: VA

address: 1015 Steger Hall, Life Science Circle

department: Biocomplexity Institute

institute: Virginia Tech

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequences were trimmed for residual adaptors and poor quality bases  (sliding window 4, phred score 25)  and length (> 36) using Trimmomatic-0.35. Non-paired reads were also filtered out.
Filtered paired end reads were alligned to mouse reference genome (GRCm38.94) using HiSAT2
Transcript Assemble and quantification of RNA-Seq was done via Stringtie, with output specific for DESeq2
DESeq2 analysis was conducted to determine normalized gene counts and differential expression (Padj < 0.05, log2-fold change > 0.5). Differential expression was conducted in a pair-wise manner between genotypes or treatments
Genome_build: GRCm38.94

source_name: BMDCs challenged with viable Aspergillus fumigatus conidia

growth_protocol: Bone marrow was extracted from the tibia and femur of wildtype and nlrx1 deficient mice. Cells were  differentiated using GM-CSF. Cells were grown  for 6 days with a medium exchange on day 3. On day 6 cells were harvested and plated at a density of 5 X10^5 cells per well (24-well format)

extract_protocol:
Cells were lysed in Buffer RLT containing BME. RNA was immediately extracted following the RNeasy Mini Kit Protocol. DNAase digestion was performed. Samples were eluted in 30ul twice.
Total RNA with RIN ≥ 8.0, was converted into a strand-specific library using Illumina’s TruSeq Stranded mRNA HT Sample Prep Kit (Illumina, RS-122-2103), for subsequent cluster generation and sequencing on Illumina's NextSeq. The library was enriched by 13 cycles of PCR, validated using Agilent TapeStation and quantitated by qPCR. Individually indexed cDNA libraries were pooled and sequenced on NextSeq

treatment_protocol: Cells were challenged with 5 X 10^5 viable Aspergillus fumigatus conidia (AF29) and incubated for various times at 37C in the presense of 5% CO2.

value: Mouse bone marrow derived dendritic cells

value: 12hrs post challenge

value: Nlrx1 deficient


title: Nlrx1 deficient BMDCs 12hrs post challenge Replicate 2


title: WT, #8/0467, 9 months old [Lemd2_8_0467_WT]

description: WT 6


title: RPE,Mertk-/-V2Tyro3-/-V2, P25, Biol rep 3 [DKO_23_3]

value: retinal pigment epithelium (RPE)

value: epithelial

value: none, direct ex-vivo use


title: ChIPseq-SET12-H3-Col-0-rep1

description: ChIP-seq data set12 of H3-Col-0 repliate1

value: anti-H3 (Abcam)


title: WT, #33/7012, 9 months old [Lemd2_33_7012_WT]

description: WT 2

value: wild-type

value: 9 months old


title: KO2, RUNX1, CD41neg

value: KO

value: bone marrow

value: RUNX1 (donation from collaborator Dr. Wu)


title: ChIPseq-SET10-PolII-CPL2-ZF-rep1

description: ChIP-seq data set10 of Pol II-CPL2-ZF repliate1

value: leaf tissue

value: 4-5 weeks


title: ChIPseq-SET10-H3-fwa-rep1

description: ChIP-seq data set10 of H3-fwa repliate1


title: WT1, RUNX1, CD41neg

value: WT

value: CD41neg HSC


title: KO1, H3K4, CD41neg


title: ChIPseq-SET11-PolII-CPL2-ZF-rep2

description: ChIP-seq data set11 of Pol II-CPL2-ZF repliate2

value: anti-Pol II (Abcam)

value: Pol II


title: ChIPseq-SET10-H3-CPL2-ZF-rep1

description: ChIP-seq data set10 of H3-CPL2-ZF repliate1


title: Nlrx1 deficient BMDCs 9hrs post challenge Replicate 1

value: Mouse bone marrow derived dendritic cells

value: 9hrs post challenge


title: Nlrx1 deficient BMDCs 9hrs post challenge Replicate 2

value: Nlrx1 deficient


title: ChIPseq-SET1-H3K4me3-JMJ14-ZF-rep1

description: ChIP-seq data set1 of H3K4me3-JMJ14-ZF repliate1

value: anti-H3K4me3 (Millipore Sigma)


title: KOMK1A

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments.  The programs used in these steps were FastQC v0.11.7,Trm Galore! v0.4.2 and cutadapt v1.9.1
The trimmed reads were aligned to the reference mouse genome version mm10 with the program STAR v2.6.1e .
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database . Read counting was done with the program featureCounts v1.6.2 from the Rsubread package.
Raw counts were normalized as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: Bigwig files containing trimed and aligned reads for each sample; matrix_ScRNAseq.tpm.txt contain raw read counts for all samples (tab separated file); matrix_ScRNAseq_noOutliers.tpm.txt contain Transcripts Per Million(TPM) counts for all samples.

extract_protocol:
HSC cells from poly(I:C)-treated WT control and RUNX1 KO mice were sorted by FACS. Cells were cultured for 2 days and harvested to extract RNA. RNA were extracted using SMART-Seq® Single Cell PLUS Kit  from Takara.( R400750)
RNA libraries for RNA-seq were prepared using SMART-Seq® Library Prep Kit (R400747) following manufacturer's protocols.

value: CD41pos HSCs

tag: cell type (differentiated)

value: MK

value: polyIC injection*4

value: 4 weeks post-injection, 2 days culture


title: KO2, H3K4, CD41neg

value: KO


title: ChIPseq-SET11-H3-fwa-rep2

description: ChIP-seq data set11 of H3-fwa repliate2

value: anti-H3 (Abcam)


title: Nlrx1 deficient BMDCs 9hrs post challenge Replicate 3


title: WT1, H3K4, CD41neg

value: bone marrow


title: KO2, H3K4, CD41pos

value: CD41pos HSC


title: ChIPseq-SET11-H3-CPL2-ZF-rep2

description: ChIP-seq data set11 of H3-CPL2-ZF repliate2

value: leaf tissue

value: 4-5 weeks


title: WT2, RUNX1, CD41pos

value: WT

value: RUNX1 (donation from collaborator Dr. Wu)


title: WT1, RUNX1, CD41pos


title: Nlrx1 deficient BMDCs 6hrs post challenge Replicate 2

value: 6hrs post challenge


title: KONMI3A

value: NMK


title: RPE, C57BL/6, P25, Biol rep 1 [B6J_23_1]

value: retinal pigment epithelium (RPE)

value: epithelial

value: none, direct ex-vivo use


title: ChIPseq-SET1-H3K27me3-MSI1-ZF-rep1

description: ChIP-seq data set1 of H3K27me3-MSI1-ZF repliate1

value: anti-H3K27me3 (Millipore Sigma)


title: WT2, RUNX1, CD41neg

value: CD41neg HSC


title: ChIPseq-SET1-H3K27me3-LHP1-ZF-rep1

description: ChIP-seq data set1 of H3K27me3-LHP1-ZF repliate1


title: KONMK1A

value: CD41pos HSCs

value: polyIC injection*4


title: Nlrx1 deficient BMDCs 12hrs post challenge Replicate 1

value: Mouse bone marrow derived dendritic cells

value: 12hrs post challenge

value: Nlrx1 deficient


title: KONMK4B

value: bone marrow

value: 4 weeks post-injection, 2 days culture


title: Nlrx1 deficient BMDCs 3hrs post challenge Replicate 2

value: 3hrs post challenge


title: ChIPseq-SET10-PolII-fwa-rep1

description: ChIP-seq data set10 of Pol II-fwa repliate1

value: leaf tissue

value: 4-5 weeks

value: anti-Pol II (Abcam)

value: Pol II


title: ChIPseq-SET1-H3K4me3-fwa-rep1

description: ChIP-seq data set1 of H3K4me3-fwa repliate1

value: anti-H3K4me3 (Millipore Sigma)


title: WTMK1B

value: MK


title: WT2, H3K4, CD41pos

value: WT

value: CD41pos HSC


title: KONMK5B

value: NMK


title: KONMK5A

value: CD41pos HSCs


title: Nlrx1 deficient BMDCs 3hrs post challenge Replicate 3


title: ChIPseq-SET1-H3K27me3-ELF7-ZF-rep1

description: ChIP-seq data set1 of H3K27me3-ELF7-ZF repliate1

value: anti-H3K27me3 (Millipore Sigma)


title: WTNMK4B

value: polyIC injection*4


title: KOMK2


title: KO1, RUNX1, CD41neg

value: KO

value: CD41neg HSC

value: RUNX1 (donation from collaborator Dr. Wu)


title: ChIPseq-SET1-H3K4me3-ELF7-ZF-rep1

description: ChIP-seq data set1 of H3K4me3-ELF7_-ZF repliate1


title: WT1, H3K4, CD41pos

value: bone marrow


title: KOMK1

value: 4 weeks post-injection, 2 days culture


title: Nlrx1 deficient BMDCs 6hrs post challenge Replicate 1

value: Mouse bone marrow derived dendritic cells

value: 6hrs post challenge

value: Nlrx1 deficient


title: KONMK3B


title: Nlrx1 deficient BMDCs 6hrs post challenge Replicate 3


title: KO1, RUNX1, CD41pos


title: KONMK4A


title: WTNMK1B


title: KONMK1


title: ChIPseq-SET1-H3K27me3-JMJ14-ZF-rep1

description: ChIP-seq data set1 of H3K27me3-JMJ14-ZF repliate1

value: leaf tissue

value: 4-5 weeks


title: WTMK1A

value: MK


title: WT BMDCs 12hrs post challenge Replicate 1

value: 12hrs post challenge

value: WT


title: WTNMK1

value: NMK


title: B1KOMK1a

value: CD41pos HSCs


title: Nlrx1 deficient BMDCs 3hrs post challenge Replicate 1

value: 3hrs post challenge


title: ChIPseq-SET1-H3-LHP1-ZF-rep1

description: ChIP-seq data set1 of H3-LHP1-ZF repliate1

value: anti-H3 (Abcam)


title: WT BMDCs 12hrs post challenge Replicate 3


title: WTNMK1A

value: polyIC injection*4


title: RNAseq-SET6-YPET-ZF-rep3

description: RNAseq data set6 of YPET-ZF replicate 3


title: WTMK2


title: WTMK4


title: ChIPseq-SET1-H3K27me3-fwa-rep1

description: ChIP-seq data set1 of H3K27me3-fwa repliate1

value: anti-H3K27me3 (Millipore Sigma)


title: KONMK1B


title: Nlrx1 deficient BMDCs prior to challenge Replicate 3

value: prior to challenge


title: B1KOMK4

value: bone marrow


title: ChIPseq-SET1-H3-ELF7-ZF-rep1

description: ChIP-seq data set1 of H3-ELF7-ZF repliate1


title: ChIPseq-SET1-H3-JMJ14-ZF-rep1

description: ChIP-seq data set1 of H3-JMJ14-ZF repliate1


title: WTMK1

value: 4 weeks post-injection, 2 days culture


title: ChIPseq-SET1-H3-MSI1-ZF-rep1

description: ChIP-seq data set1 of H3-MSI1-ZF repliate1


title: B1KOMK1


title: WTNMK4A


title: RNAseq-SET6-fwa-rep18

description: RNAseq data set6 of fwa replicate18


title: WTNMK4


title: WT BMDCs 6hrs post challenge Replicate 3

value: Mouse bone marrow derived dendritic cells


title: WT BMDCs 12hrs post challenge Replicate 2


title: RNAseq-SET6-YPET-ZF-rep2

description: RNAseq data set6 of YPET-ZF replicate 2


title: Nlrx1 deficient BMDCs prior to challenge Replicate 1


title: WTNMK3A


title: WTNMK2


title: Nlrx1 deficient BMDCs prior to challenge Replicate 2


title: WT BMDCs 9hrs post challenge Replicate 2

value: 9hrs post challenge


title: WT BMDCs 9hrs post challenge Replicate 3


title: RNAseq-SET6-YPET-ZF-rep1

description: RNAseq data set6 of YPET-ZF replicate 1


title: WT BMDCs 9hrs post challenge Replicate 1


title: B1KONMK1a


title: B1WTMK2b


title: B1KONMK3b


title: WTNMK3


title: WT BMDCs 6hrs post challenge Replicate 2

value: 6hrs post challenge


title: WTNMK2B


title: ChIPseq-SET1-H3-fwa-rep1

description: ChIP-seq data set1 of H3-fwa repliate1

value: leaf tissue


title: B1KONMK1b


title: RNAseq-SET6-fwa-rep17

description: RNAseq data set6 of fwa replicate17

value: 4-5 weeks


title: RNAseq-SET5-ZF-SUVH2-rep1

description: RNAseq data set5 of ZF-SUVH2 replicate 1


title: RNAseq-SET5-fwa-rep15

description: RNAseq data set5 of fwa replicate15


title: B1KONMK3a


title: WT BMDCs prior to challenge Replicate 3


title: B1KONMK2b


title: B1KWTMK1b

value: MK


title: RNAseq-SET5-ZF-SUVH2-rep3

description: RNAseq data set5 of ZF-SUVH2 replicate 3


title: B1KOMK3


title: WT BMDCs 3hrs post challenge Replicate 3


title: WT BMDCs 6hrs post challenge Replicate 1


title: WT BMDCs prior to challenge Replicate 1


title: B1WTNMK1b

description:
B1WTNMK1b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B1WTNMK1a

description:
B1WTNMK1a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B1WTNMK3

description:
B1WTNMK3 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET4-JMJ18-ZF-rep3

description: RNAseq data set4 of JMJ18-ZF replicate 3


title: B1KONMK5


title: WT BMDCs 3hrs post challenge Replicate 2


title: B1KONMK2a


title: B1WTMK1


title: B1WTNMK1

description:
B1WTNMK1 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B1WTMK1a


title: B1WTMK2a


title: Input, rep1

city: Beijing

first: Quancan

last: Hou

address: Xueyuan road No. 30

country: China

institute: University of Science and Technology Beijing

data_processing:
ChIP-seq reads with more than 10% unknown bases (N bases) and reads with more than 50% of low-quality bases (quality value ≤ 5) in one read were filtered using fastp.
Clean reads  were aligned to the maize B73 V4 genome using Bowtie2 version 2.4.0. Only uniquely mapping reads with at most two mismatches were retained.
Duplicated reads generated by PCR during the library construction were removed using samtools version 1.10.
Peaks were called uing MACS v2.2.4 with the significance cut-off q-value <=0.01
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were renormalized (reads per genomic content) and reformatted into the bigWig file format using deeptools version 2.0.
Assembly: B73
Supplementary files format and content: bigWig

organism: Zea mays

source_name: Anther

growth_protocol: Maize plants were grown in Beijing (40°05′N, 116°37′E) from May to October under nature conditions

extract_protocol:
Chromatin was sonicated using a Bioruptor Plus UCD-300 sonicator, immunoprecipated DNA was sonicated using a E220 focused-ultrasonicator (Covaris)
Immunoprecipated DNA was sonicated to an average size of 200bp and end-repaired using an End-it DNA End repair kit (Epicentre, ER0720). Fragments were ligated with the adaptor and amplified using 15 cycles on the thermocycler using illumina primers (Yeasen, 12613ES02). Post amplification libraries were size selected at 250-450bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Collected anthers in developmental stages 9 to 10 were crosslinked in PBS containing 1% formaldehyde for 10 min

value: Anther

tag: cell line

value: Anther cells

value: Mixed anther cells

value: proLOB30:GFP-LOB30 in Hi II background


title: B1KOMK1b

value: CD41pos HSCs


title: RNAseq-SET6-fwa-rep16

description: RNAseq data set6 of fwa replicate16


title: B1WTNMK4b

description:
B1WTNMK4b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: NMK


title: WT BMDCs 3hrs post challenge Replicate 1

value: 3hrs post challenge

value: WT


title: B1WTMK2

value: polyIC injection*4


title: RNAseq-SET5-ZF-SUVH2-rep2

description: RNAseq data set5 of ZF-SUVH2 replicate 2


title: B1WTNMK2b

description:
B1WTNMK2b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: bone marrow


title: KOMK1B

value: 4 weeks post-injection, 2 days culture


title: B1WTNMK2a

description:
B1WTNMK2a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET5-fwa-rep13

description: RNAseq data set5 of fwa replicate13


title: RNAseq-SET4-fwa-rep12

description: RNAseq data set4 of fwa replicate12


title: NC, rep1

value: Binding control magnetic agarose (Chromotek, Cat# bmab-20 )


title: WT BMDCs prior to challenge Replicate 2

value: Mouse bone marrow derived dendritic cells

value: prior to challenge


title: RNAseq-SET4-JMJ18-ZF-rep2

description: RNAseq data set4 of JMJ18-ZF replicate 2

value: leaf tissue


title: RNAseq-SET4-fwa-rep11

description: RNAseq data set4 of fwa replicate11

value: 4-5 weeks


title: LOB30IP, rep3

value: GFP-Trap magnetic agarose (Chromotek, Cat# gtma-22)


title: RNAseq-SET4-JMJ18-ZF-rep1

description: RNAseq data set4 of JMJ18-ZF replicate 1


title: RNAseq-SET3-HD2C-ZF-rep3

description: RNAseq data set3 of HD2C-ZF replicate 3


title: B2KONMK7b

description:
B2KONMK7b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: LOB30IP, rep2

value: Anther

value: GFP-Trap magnetic agarose (Chromotek, Cat# gtma-21)


title: RNAseq-SET3-HD2C-ZF-rep2

description: RNAseq data set3 of HD2C-ZF replicate 2


title: NC, rep2

value: Anther cells

value: Mixed anther cells


title: RNAseq-SET3-HD2C-ZF-rep1

description: RNAseq data set3 of HD2C-ZF replicate 1


title: LOB30IP, rep1

value: proLOB30:GFP-LOB30 in Hi II background

value: GFP-Trap magnetic agarose (Chromotek, Cat# gtma-20)


title: B2KOMK1a

description:
B2KOMK1a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: CD41pos HSCs

value: MK


title: B1WTNMK4a

description:
B1WTNMK4a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: NMK

value: polyIC injection*4


title: B2KONMK3a

description:
B2KONMK3a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: bone marrow

value: 4 weeks post-injection, 2 days culture


title: RNAseq-SET3-HD2B-ZF-rep3

description: RNAseq data set3 of HD2B-ZF replicate 3


title: B2KONMK7a

description:
B2KONMK7a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B2KONMK4a

description:
B2KONMK4a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RA9 M2

city: Dublin 2

first: Megan

middle: Mary

last: Hanlon

state: Dublin

address: Trinity biomedical sciences institute, trinity college dublin

department: School of Medicine

country: Ireland

institute: Molecular Rheumatology research group

data_processing:
Raw read quality was evaluated using FastQC before reads were trimmed for adaptors and sequence quality. Trimmed reads were aligned to human CRCh38.84 reference genome using STAR RNA-seq aligner.
Aligned reads were quantified for each gene. Aligned data were evaluated for quality using several quality metrics (e.g. mapping rate, coverage) and visually inspected for samples deviating from the population across multiple metrics and principal component analysis.
Assembly: Trimmed reads were aligned to human CRCh38.84 reference genome using STAR RNA-seq aligner
Supplementary files format and content: tab-delimited text files of TPM for each Sample

organism: Homo sapiens

source_name: Primary human cells

growth_protocol: Pure CD14+ monocytes were magnetically sorted from RA peripheral blood mononuclear cells.

extract_protocol:
High quality RNA was isolated from RA polarised monocyte-derived macrophages using the RNeasy kit (QIAGEN) and the purity of RNA samples was assessed using a NanoDrop 2000 spectrophotometer (ThermoFisher).
RNA samples were reverse transcribed and sequence libraries were generated by Janssen Pharmaceutical, Spring House, PA, USA, using the NuGen Ovation Universal RNA-seq System. The resulting sequencing libraries were analysed using the Cali-per LabChip GX and quantified using KAPA qPCR.

treatment_protocol:
CD14+ monocytes were seeded at a density of 2 x 106 cells/well in a 6 well plate and cultured in complete RPMI supplemented with M-CSF (50 ng/mL) (PeproTech, UK) for 8 days to derive in vitro macrophage cultures
Macrophages were then polarised for 24hr to either ‘M1-like’ macrophages using LPS (100 ng/mL) (Enzo Life Sciences, Belgium) or IFNϒ (20 ng/mL) (PeproTech, UK) or ‘M2-like’ macrophages using IL-4 (20 ng/mL) (PeproTech, UK).

value: Primary human cells

value: Polarised monocyte-derived macrophages

tag: disease state

value: Rheumatoid Arthritis

value: 24 hrs IL-4 (20ng/ml)

value: Day 8


title: B2KONMK2b

description:
B2KONMK2b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

tag: tissue


title: hDPSCs, Nutlin-3

city: Seoul

first: SoYoung

last: Park

state: Korea,Seoul

address: Seoul, Republic of Korea,, 1 Gwanak-ro, Gwanak-gu, Seoul, 86-509

country: South Korea

institute: Seoul National University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trim Galore version 0.5.0 was used to remove adapter sequences. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed reads were aligned to human genome (GRCh38) using Bowtie2 version 2.3.4.1 parameter set --maxins 5000 --very-sensitive --no-discordant --no-mixed --no-unal --mm. Duplicate reads were removed using MarkDuplicates in Picard version 1.118.
Peaks were called in the aligned sequence data using a model-based analysis of ATAC-seq MACS2 version 2.1.1. The following parameters were used: macs2 callpeak --bdg --nolambda --keep-dup all --broad. Among the called peaks, the peaks overlapping with ENCODE blacklisted regions were removed.
ChIPseeker version 1.20.0 a bioconductor package within R version 3.6.0 to facilitate batch annotation of enriched peaks.
Assembly: GRCh38
Supplementary files format and content: bigWig, bedGraph

source_name: hDPSCs

growth_protocol: Human dental pulp-derived mesenchymal stromal cells (hDPSCs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C °C

extract_protocol:
Prepare cells using LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems). Resuspend nuclei in transposition reaction mix. Incubate the transposition reaction for 30min at 37°C. Immediately following transposition, purify using a Qiagen MinElute PCR purification Kit.
Amplify transposed DNA fragment using Nextera DNA Flex kit. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA) and qualified using Bioanalyzer (Agilent technologies).
bulk ATAC-seq

treatment_protocol: To detect the osteogenic differentiation capability of hDPSCs, they were cultured in 50 μg/mL ascorbic acid (Sigma-Aldrich) and 10 mM β-glycerophosphate (Sigma-Aldrich) in DMEM containing 10% FBS and 1% penicillin-streptomycin.

tag: agent

value: hDPSCs

value: osteogenic differentiation

value: Day 7


title: B2KOMK1b

description:
B2KOMK1b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B2KONMK4b

description:
B2KONMK4b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET4-fwa-rep10

description: RNAseq data set4 of fwa replicate10

value: leaf tissue

tag: developmental stage

value: 4-5 weeks

tag: strain


title: Input, rep2

value: Anther

value: Anther cells

value: Mixed anther cells

value: proLOB30:GFP-LOB30 in Hi II background


title: RNAseq-SET5-fwa-rep14

description: RNAseq data set5 of fwa replicate14


title: RNAseq-SET3-HD2B-ZF-rep2

description: RNAseq data set3 of HD2B-ZF replicate 2


title: B2KONMK2a

description:
B2KONMK2a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: CD41pos HSCs

value: NMK

value: polyIC injection*4


title: B2KONMK3b

description:
B2KONMK3b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: bone marrow

value: 4 weeks post-injection, 2 days culture


title: RA9 M1

value: Primary human cells

value: Polarised monocyte-derived macrophages

value: Rheumatoid Arthritis

value: 24 hrs LPS (100ng/ml) and IFNg (20ng/ml)


title: B2KONMK1

description:
B2KONMK1 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: hDPSCs, Control

value: Control

value: hDPSCs

value: osteogenic differentiation


title: RNAseq-SET3-HD2B-ZF-rep1

description: RNAseq data set3 of HD2B-ZF replicate 1

value: leaf tissue

value: 4-5 weeks


title: B2KONMK2

description:
B2KONMK2 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B2KONMK1a

description:
B2KONMK1a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET3-HD2A-ZF-rep1

description: RNAseq data set3 of HD2A-ZF replicate 1


title: B2WTMK3b

description:
B2WTMK3b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: MK


title: RNAseq-SET3-fwa-rep7

description: RNAseq data set3 of fwa replicate7


title: B2KONMK1b

description:
B2KONMK1b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RA5 M2

value: 24 hrs IL-4 (20ng/ml)

value: Day 8


title: RNAseq-SET3-ELF7-ZF-rep2

description: RNAseq data set3 of ELF7-ZF replicate 2


title: RA8 M2


title: RNAseq-SET3-HD2A-ZF-rep3

description: RNAseq data set3 of HD2A-ZF replicate 3


title: RNAseq-SET3-HD2A-ZF-rep2

description: RNAseq data set3 of HD2A-ZF replicate 2


title: RNAseq-SET3-fwa-rep8

description: RNAseq data set3 of fwa replicate8


title: RA7 M1


title: RNAseq-SET3-fwa-rep9

description: RNAseq data set3 of fwa replicate9


title: RA6 M2


title: B2WTMK3a

description:
B2WTMK3a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: CD41pos HSCs


title: B2WTMK1a

description:
B2WTMK1a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RA7 M2


title: RA5 M1


title: RA6 M1


title: B2WTMK2

description:
B2WTMK2 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RA8 M1


title: B2wtmk1b

description:
B2WTMK1b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET2-MSI1-ZF-rep3

description: RNAseq data set2 of MSI1-ZF replicate 3


title: RNAseq-SET3-ELF7-ZF-rep1

description: RNAseq data set3 of ELF7-ZF replicate 1


title: B2WTNMK8b

description:
B2WTNMK8b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: NMK


title: RNAseq-SET3-ELF7-ZF-rep3

description: RNAseq data set3 of ELF7-ZF replicate 3


title: B2WTNMK8a

description:
B2WTNMK8a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: polyIC injection*4


title: RA2 M2


title: RA3 M1


title: RNAseq-SET2-JMJ14-ZF-rep3

description: RNAseq data set2 of JMJ14-ZF replicate 3


title: B2WTNMK7b

description:
B2WTNMK7b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: bone marrow


title: RA3 M2


title: B2WTMK1

description:
B2WTMK1 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: 4 weeks post-injection, 2 days culture


title: RNAseq-SET2-JMJ14-ZF-rep2

description: RNAseq data set2 of JMJ14-ZF replicate 2


title: RNAseq-SET2-MSI1-ZF-rep2

description: RNAseq data set2 of MSI1-ZF replicate 2


title: RA1 M2

value: Primary human cells


title: B2WTMK4

description:
B2WTMK4 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET2-JMJ14-ZF-rep1

description: RNAseq data set2 of JMJ14-ZF replicate 1


title: RA4 M2

value: Polarised monocyte-derived macrophages


title: RA4 M1

value: Rheumatoid Arthritis


title: B2WTNMK6b

description:
B2WTNMK6b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B2WTNMK7a

description:
B2WTNMK7a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B2WTNMK6a

description:
B2WTNMK6a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET2-HDA6-ZF-rep2

description: RNAseq data set2 of HDA6-ZF replicate 2


title: RNAseq-SET2-HDA6-ZF-rep3

description: RNAseq data set2 of HDA6-ZF replicate 3


title: RA2 M1

value: 24 hrs LPS (100ng/ml) and IFNg (20ng/ml)


title: RNAseq-SET2-MSI1-ZF-rep1

description: RNAseq data set2 of MSI1-ZF replicate 1


title: B2WTNMK5b

description:
B2WTNMK5b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B2WTNMK5a

description:
B2WTNMK5a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET2-HDA6-ZF-rep1

description: RNAseq data set2 of HDA6-ZF replicate 1


title: Human_5

city: Maastricht

first: Vanessa

last: LaPointe

address: Universiteitssingel 40

country: Netherlands

institute: MERLN Institute

data_processing:
BCL files resulting from sequencing were transformed to FASTQ and read 1 was used to identify the Illumina library index and CEL-seq sample barcode.
Read 2 was aligned to the specific RefSeq reference genome of each species using STAR genome aligner (Dobin et al. 2013)
The data from all samples were loaded in R (version 4.1.2) (R Core Team 2013) to perform analysis.
Assembly: Human: Hg38
Assembly: Sheep: ARS-UI_Ramb_v2.0
Assembly: Rabbit: OryCun2.0
Supplementary files format and content: _total.ReadCounts.tsv final datasets containing the read counts for all genes across each species

source_name: Cornea

growth_protocol: All human corneas were stored up to 22 days in organ culture media at 31 °C and had a minimum endothelial cell density of 2300 cells/mm2. Organ culture media comprised the following: minimum essential medium (MEM) supplemented with 20 mM HEPES, 26 mM sodium bicarbonate, 2% (v/v) newborn calf serum (Thermo Fisher Scientific), 10 IU/mL penicillin, 0.1 mg/mL streptomycin and 0.25 μg/mL amphotericin.

extract_protocol:
Corneal endothelium samples were extracted from the tissue and sequenced as follows:  Isolation of human corneal endothelium  Of the five human corneal endothelial samples, four were discarded peripheral endothelial rims (1.5 mm wide) resulting from tissue preparation for Descemet’s membrane endothelial Keratoplasty (DMEK) according to clinical practice (Català et al. 2020) and one (Human 5) was a whole endothelium stripped from a cornea deemed unsuitable for transplant (Table 1).     The four endothelial rims were lysed in 300 μL trizol within 48 h after tissue preparation. From the whole cornea, the complete endothelium was manually stripped following lysis in 300 μL trizol. Briefly, the cornea was vacuum-fixed in a punch base (e.janach) endothelial-cell side up and trephined with a 10 mm Ø corneal punch at a fixed depth of 100 μm (e.janach). To delimit the endothelial trephined line, the cornea was stained with a trypan blue solution (0.4%) for 30 s, and washed with balanced salt solution (BSS) ophthalmic irrigation solution. The corneal endothelium was then gently lifted using a DMEK cleavage hook (e.janach), fully stripped using angled McPherson tying forceps, and immediately transferred to trizol. All sample lysates were stored at -80 °C until further use.    Isolation of sheep corneal endothelium  All samples (n=5) were obtained from Texel sheep used for a dorsal titanium implant study from the animal facility at Maastricht University (Table 1). Five eyes were enucleated from 1 to 2-year-old female Texel sheep within 4 h of sacrifice, and corneoscleral disks were excised from whole ocular gloves. Corneal endothelial cells were enzymatically treated and scrapped from the corneoslceral disks because stripping of the endothelium proved not successful due to the tissue characteristics. For this purpose, corneoscleral disks were rinsed with Dulbecco's phosphate buffered saline (DPBS), vaccum-fixed in a punch base (e.janach) endothelial-side up and treated with approximately 150 μL of StemPro Accutase (Thermo Fisher Scientific) for 20 min at ambient temperature. Corneal endothelial cells were then gently scraped using a DMEK cleavage hook (e.janach) and rinsed off the corneoscleral disk with approximately 2 mL of MEM (Thermo Fisher Scientific). The cell suspension was then transferred to a 15 mL tube, centrifuged at 800 × g for 5 min and lysed in 300 μL trizol. All sample lysates were stored at -80 °C until further use.    Isolation of rabbit corneal endothelium  Eyes were obtained from New Zealand White rabbits used for other experimental purposes from the Utrecht University animal facility (n=3) and MSD Animal testing facility (n=2) in Boxmeer, the Netherlands (Table 1). Eyes were enucleated 30 min to 4 h after sacrifice, corneoscleral disks were excised from whole ocular globes, and corneal endothelium stripped. In brief, corneoscleral disks were rinsed with PBS, vacuum-fixed in a punch base endothelial-side up and trephined with a 10 mm Ø corneal punch at a fixed depth of 100 μm. To delimit the endothelial trephined line, the cornea was stained with a trypan blue solution (0.4%) for 30 s, and washed with BSS ophthalmic irrigation solution. The corneal endothelium was then gently lifted using a DMEK cleavage hook, fully stripped using angled McPherson tying forceps, and immediately transferred to 300 μL trizol. All sample lysates were stored at -80 °C until further use.
RNA isolation and bulk RNA sequencing  RNA isolation was performed following trizol isolation procedure, and RNA integrity was assessed with a 2100 Bioanalyzer (Agilent). RNA sequencing was performed at Single Cell Discoveries (Utrecht, the Netherlands). Libraries were prepared following CEL-seq2 protocol (Hashimshony et al. 2016) to enable sample multiplexing. Paired-end sequencing was performed on Illumina Nextseq500, high output 2 × 75 bp run mode, at a sequencing depth of 20 million reads/sample.     Data analysis and pre-processing  BCL files resulting from sequencing were transformed to FASTQ and read 1 was used to identify the Illumina library index and CEL-seq sample barcode. Read 2 was aligned to the specific RefSeq reference genome of each species, namely: hg19 for human, OryCun2.0 for rabbit, and ARS-UI_Ramb_v2.0 for sheep using STAR genome aligner (Dobin et al. 2013).   The data from all samples were loaded in R (version 4.1.2) (R Core Team 2013) to perform analysis. Gene homology mapping from rabbit and sheep to human was performed using the orthogene R-package (version 1.1.0) with the g:profiler method (Raudvere et al. 2019). The three datasets were combined and only genes with homologs in all three species were included in the downstream analyses. Once the data was combined quantile normalization was performed using the limma package (version 3.52.2) (Ritchie et al. 2015).

treatment_protocol: Not applicable to this study

tag: sample number

tag: gender - age

value: Female - 67 years

tag: dissection

value: Endothelium


title: RNAseq-SET2-fwa-rep6

description: RNAseq data set2 of fwa replicate 6


title: B2WTNMK2b

description:
B2WTNMK2b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

tag: cell type

tag: genotype

tag: treatment


title: Human_4

value: Male - 57 years


title: RA1 M1


title: B2WTNMK2a

description:
B2WTNMK2a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: RNAseq-SET2-fwa-rep5

description: RNAseq data set2 of fwa replicate 5

value: leaf tissue


title: B2WTNMK1b

description:
B2WTNMK1b - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: nanoCAGE-seq_H929

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
nanoCAGE-seq libraries were sequenced on the Illumina NextSeq platform and aligned to the hg38 reference genome with STAR. All browser tracks are visualized on the WashU Epigenome Browser70.
Assembly: hg38
Supplementary files format and content: reads are aligned to hg38

source_name: H929 cancer cell line

growth_protocol: All cell lines were grown under the optimal condition according to ATCC handling guidelines for each cell line.

extract_protocol: To identify transcription start site locations, we generated nanoCAGE-seq libraries following published methods(Jang, Hyo Sik et al. 2019; Salimullah, Md et al. 2011). In brief, we extracted mRNA from cancer cell lines using Dynabeads mRNA DIRECT Purification Kit (ThermoFisherScientific, 61011). 5'-capped mRNA was enriched through Terminator exonuclease digestion (Lucigen, TER51020). Afterwards, we processed 25ng of Terminator-treated mRNA following standard nanoCAGE protocol to capture 5' ends of mRNA via template-switching technology.

treatment_protocol: No treatment was applied to the cell lines before profile.

tag: cancer type

value: Plasma cell myeloma


title: RNAseq-SET2-fwa-rep4

description: RNAseq data set2 of fwa replicate 4

value: 4-5 weeks


title: Human_2

value: Male - 68 years


title: Human_3

value: Female - 73 years


title: Human_1

value: Male - 66 years


title: mice high dose SAR rep3 [H3]

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

description:
read_count.M_vs_H.DESeq.DE_results
GEO_submission_processed data

data_processing:
We applied DEGSeq2 algorithm to filter the differentially expressed genes, after the significant analysis under the following criteria: i) |log2FC|>1;ii) Pvalue<0.05.
Assembly: mm9

source_name: liver

growth_protocol: Model group and SAR group were induced nonalcoholic fatty liver disease by MCD-diet, normal group were given same dose normal saline

extract_protocol:
Total RNA was extracted from liver tissues with Trizol reagent
NEBNext Ultra TM RNA Library Prep Kit (NEB #E7490), AMPure XP system

treatment_protocol: SAR group were treated with SAR

value: liver

value: high dose SAR group


title: mice high dose SAR rep2 [H2]


title: RNAseq-SET1-LHP1-ZF-rep2

description: RNAseq data set1 of LHP1-ZF replicate 2


title: B2WTNMK4

description:
B2WTNMK4 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: bone marrow

value: CD41pos HSCs

value: NMK

value: polyIC injection*4

tag: time


title: nanoCAGE-seq_SR

data_processing:
nanoCAGE-seq libraries were sequenced on the Illumina NextSeq platform and aligned to the hg38 reference genome with STAR. All browser tracks are visualized on the WashU Epigenome Browser70.
Assembly: hg38
Supplementary files format and content: reads are aligned to hg38
Library strategy: nanoCAGE

source_name: SR cancer cell line

value: SR

value: ALK-positive anaplastic large cell lymphoma


title: RNAseq-SET1-LHP1-ZF-rep3

description: RNAseq data set1 of LHP1-ZF replicate 3


title: nanoCAGE-seq_SNU475

source_name: SNU475 cancer cell line

value: Adult hepatocellular carcinoma


title: mice model rep3 [M3]

description:
read_count.N_vs_M.DESeq.DE_results
GEO_submission_processed data

value: model group (MCD diets)


title: RNAseq-SET1-fwa-rep3

description: RNAseq data set1 of fwa replicate 3


title: mice high dose SAR rep1 [H1]


title: nanoCAGE-seq_H716

source_name: H716 cancer cell line

value: A cecum adenocarcinoma cell line established from a metastasis of Ascites


title: B2WTNMK1a

description:
B2WTNMK1a - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.

value: 4 weeks post-injection, 2 days culture


title: mice model rep2 [M2]


title: RNAseq-SET1-fwa-rep2

description: RNAseq data set1 of fwa replicate 2

source_name: Arabidopsis leaf tissue

value: leaf tissue


title: B2WTNMK2

description:
B2WTNMK2 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: B2WTNMK1

description:
B2WTNMK1 - processed data to be provided
This sample is not represented in matrix_ScRNAseq_noOutliers.tpm.txt or matrix_ScRNAseq.tpm.txt.


title: mice wt rep3 [N3]

value: normal group


title: CD41neg, KO3

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments.  The programs used in these steps were FastQC v0.11.7,Trm Galore! v0.4.2 and cutadapt v1.9.1
The trimmed reads were aligned to the reference mouse genome version mm10 with the program STAR v2.6.1e .
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database . Read counting was done with the program featureCounts v1.6.2 from the Rsubread package.
Raw counts were normalized as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: Bigwig files containing trimmed and aligned reads for each sample; matrix_RNAseq.feat contain raw read counts for all samples (tab separated file); matrix_RNAseq.tpm contain Transcripts Per Million(TPM) counts for all samples.

extract_protocol:
HSC cells from poly(I:C)-treated WT control and RUNX1 KO mice were sorted by FACS. RNA were extracted using miRNeasy Micro Kit (Qiagen, 217084).
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) following manufacturer's protocols.

value: CD41ned HSC

value: 4 weeks post-injection


title: mice model rep1 [M1]


title: RNAseq-SET1-fwa-rep1

description: RNAseq data set1 of fwa replicate 1

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
BS-sPCR reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Assembly: tair10
Supplementary files format and content: bigWig

value: 4-5 weeks


title: CD41neg, KO1


title: nanoCAGE-seq_H2228

source_name: H2228 cancer cell line

value: Lung adenocarcinoma


title: RNAseq-SET1-CPL2-ZF-rep3

description: RNAseq data set1 of CPL2-ZF replicate 3


title: mice wt rep2 [N2]

value: liver


title: nanoCAGE-seq_H2110

source_name: H2110 cancer cell line

value: A lung non-small cell carcinoma cell line established from a metastasis of Pleural effusion


title: RNAseq-SET1-CPL2-ZF-rep2

description: RNAseq data set1 of CPL2-ZF replicate 2


title: nanoCAGE-seq_DMS53

source_name: DMS53 cancer cell line

value: Lung small cell carcinoma


title: RNAseq-SET1-LHP1-ZF-rep1

description: RNAseq data set1 of LHP1-ZF replicate 1


title: mice wt rep1 [N1]


title: nanoCAGE-seq_SKMEL2

source_name: SKMEL2 cancer cell line

value: A Melanoma cell line established from a metastasis of Thigh skin


title: RNAseq-SET1-CPL2-ZF-rep1

description: RNAseq data set1 of CPL2-ZF replicate 1


title: nanoCAGE-seq_DMS454

source_name: DMS454 cancer cell line


title: CD41pos, KO2

source_name: bone marrow

value: bone marrow

value: CD41pos HSC

value: polyIC injection*4


title: Rabbit_5

organism: Oryctolagus cuniculus

value: Female - 4 months

value: Endothelium


title: nanoCAGE-seq_COV413a

source_name: COV413a cancer cell line

value: A human ovarian epithelial-serous carcinoma cell line established from a metastasis of the sigmoid colon


title: WT-2

first: zhongyi

last: wang

state: Beijing

address: No.2 Yuanmingyuan Xi Lu

institute: CAU(China Agricultural University)

data_processing:
Analyses of the transcriptome data were performed on the allwegene cloud (https://cloud.allwegene.com/project/list)
STAR software used to compare the sequenced Reads to the reference genome(Alexander Dobin, Carrie A.Davis, et al. (2013)."STAR:ultrafastuniversalRNA-seqaligner.")
Differentially expressed genes (DEGs) were calculated using DESeq2 (Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. doi:10.1186/s13059-014-0550-8.). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. The false discovery rate (FDR) less than 0.05 and the fold change larger than 2 as were set as the threshold.
ChineseLong_v2
Excel files include FPKM values for each Sample

organism: Cucumis sativus

source_name: fertilized ovary

extract_protocol:
The RNA of the sample was harvested using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary with stigma

tag: Stage

value: 32h after pollination

value: wild type

value: fertilized ovary


title: WT-3


title: Rabbit_4


title: WT-1


title: CD41pos, KO1

value: 4 weeks post-injection


title: nanoCAGE-seq_H1623

source_name: H1623 cancer cell line

value: A lung adenocarcinoma cell line established from a metastasis of lymph node


title: CD41pos, KO3


title: CD41neg, WT3

value: CD41ned HSC


title: Rabbit_3

value: Male - 9 months


title: Nlrx1 deficient BEAS-2B 3hr Replicate 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequences were trimmed for residual adaptors and poor quality bases (sliding window 4, phred score 25) and length (> 36) using Trimmomatic-0.35. Non-paired reads were also filtered out.
Filtered paired end reads were aligned and counted to the human reference genome (GRCh38.96) using STAR’s GeneCounts quantitation mode.
DESeq2 analysis was conducted to determine normalized gene counts and differential expression (Padj < 0.05, log2-fold change > 0.5). Differential expression was conducted in a pair-wise manner between genotypes or treatments
Genome_build: GRCh38.96

source_name: BEAS-2B Airway Epithelial Cells

growth_protocol: BEAS-2B airway epithelial cells were cultures according to standard protocols in RPMI1640 in 10% FBS plus Pen/Strep at 37C in the presence of 5% carbon dioxide. Cells were plated at a density of 5 X10^5 cells per well (24-well format) and allowed to equilibrate for 24 hours prior to challenge.

treatment_protocol: Cells were challenged with 5 X 10^5 viable Aspergillus fumigatus conidia (AF29) and incubated for various times at 37C in the presence of 5% CO2.

value: BEAS-2B Airway Epithelial Cells

tag: challenge

value: Aspergillus fumigatus conidia


title: Rabbit_2

source_name: Cornea


title: Nlrx1 deficient BEAS-2B 3hr Replicate 3


title: Rabbit_1


title: CD41pos, WT4


title: M-3 (Csalc-3)

value: Csalc-/-


title: CD41pos, WT3

value: bone marrow


title: CD41neg, WT2


title: M-1 (Csalc-1)


title: Nlrx1 deficient BEAS-2B 0hr Replicate 3


title: M-2 (Csalc-2)


title: Nlrx1 deficient BEAS-2B 0hr Replicate 2


title: Nlrx1 deficient BEAS-2B 3hr Replicate 1


title: 710 WT NT

city: Bryan

first: Raquel

last: Sitcheran

state: TX

address: 8447 Riverside parkway

institute: Texas A&M University School of Medicine

data_processing:
Align sequences to genome and make transcriptome index: Salmon (version 1.4.0-gompi-2020b)
Calculate differential gene expression from transcriptome index: DESeq2 (version 1.32.0)
Supplementary files format and content: Mus_musculus (GRCm39)
Supplementary files format and content: differential expression data from DESeq2 output. Shows log2fold change and pValue: results_KO_M0.csv, results_KOM2vsWTM2.csv

source_name: Bone marrow derrived macrophages

growth_protocol: For bone marrow derrived macrophages, bone marrow was isolated from the femurs and tibiae of mice. After red blood cell lysis using ACK buffer, marrow cells were then cultured for 7 days in the presence of 30% conditioned media harvested from L929 cells (a source of MCSF) to enrich for macrophages. On day 7, cells were lifted and re-plated into well dishes in 5% L929 conditioned media for IL-4 treatment experiments.

extract_protocol:
Total RNA was extracted from Frozen Cell Pellet samples using Qiagen RNeasy Plus Mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with PBS (Mock) or stimulated with 20 ng/ml IL-4 PeproTech (214-14) for 6 hours.

tag: age

value: 12 weeks

tag: Sex

value: Female

value: Bone marrow derrived macrophages

value: WT

value: PBS


title: 710 WT IL4

value: 20ng/mL IL-4 6hr


title: Nlrx1 deficient BEAS-2B 0hr Replicate 1

tag: cell line


title: 709 NIK KO NT

value: NIK KO


title: LSKCD150+ HSCs, KO mice

description: 10X Genomic Chromium

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

extract_protocol:
About 10,000 freshly sorted LSKCD150+HSCs were performed 10x scRNA sequencing by 10X Genomic Chromium under Fluidigm C1™ Single-Cell Auto Prep System.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

tag: tissue

value: RUNX1 KO


title: 24 hour rep 3

city: Gainesville

first: Matias

last: Kirst

state: MA

address: 2033 Mowry Road, Room 320

department: School of Forest, Fisheries, and Geomatics Sciences

institute: University of FLorida

data_processing:
The Poplar LCO-treatment time course data set was analyzed to quantify and normalize gene expression with Kallisto/Sleuth for the Populus trichocarpa v3.1 genome annotation (Bray et al. 2016; Pimentel et al. 2017; Tuskan et al. 2006). First, Kallisto was used to align the data and quantify expression for individual transcripts for each replicate data set. Sleuth was subsequently applied to infer appropriate per-gene expression levels from the results per-transcript. The fraction of aligned reads across all replicates of all time points averaged 48% and varied between 28-79%. The resulting per-gene TPM expression levels were subsequently log-transformed and quantile-normalized across the time course in Matlab. The replicates had a correlation of 0.93-0.99 and were analyzed with a principal components analysis to identify potential outliers. Based on such findings and poor alignment rates <= 22%, one 30 min and one 2 hr time-point replicate were removed.
Genome_build: Populus trichocarpa v3.1 genome annotation (Bray et al. 2016; Pimentel et al. 2017; Tuskan et al. 2006)
Supplementary_files_format_and_content: A txt file containing the normalized gene expresion data: gene_expression_est_cnt_reordered_qnorm.txt

organism: Populus tremula x Populus alba

source_name: root

growth_protocol: Shoot tips (about 10-15 mm long) cut from in vitro grown Populus tremula × alba INRA clone 717-1B4 were placed aseptically on Murashige and Skoog media with vitamins (PhytoTech Labs-M519) supplemented with 0.1 g/L myo-inositol (PhytoTech Labs-I703), 0.25 g/L MES (PhytoTech Labs-M825), 2% (w/v) sucrose (PhytoTech Labs-S391) and solidified with 0.8% agar (PhytoTech Labs-A296). The pH of the medium was adjusted to 5.8 with KOH before autoclaving. Explants were placed in a growth chamber under long-day conditions (16 hours light/8 hours darkness, 24 °C, 65% relative humidity, and 100 μmol m−2 s−1 photosynthetic photon flux). Once the shoot tips were rooted, and the root was at least 25 mm long, plantlets were transferred to square plates (22.5 x 22.5 cm) containing Woody Plant Medium with reduced nitrogen (0.5 mM) and phosphate (7 μM), and 1.3 g/l calcium gluconate (Lloyd and McCown 1980). Plantlets were grown vertically for ten days in the growth chamber.

extract_protocol:
RNA extraction was performed as described previously (Chang et al. 1993).
Libraries were prepared using 0.5 μg of RNA in the NEBNext® UltraTM Directional RNA Library Prep Kit following the supplier’s instructions (New England Biolabs, Ipswich, MA, USA).
For each library, reads obtained after sequencing with two Illumina HiSeq3000 (2×100 cycles) and one Miseq were used for the gene expression analyses.

treatment_protocol: Next, 3 hours after growth chamber dawn, plates were flooded to immerse roots in a 10-8 M solution of purified Rhizobium sp. IRBG74 LCOs or a control solution (0.005% ethanol) for 1 hour. After 1 hour, the solution was poured off, and plants returned to the growth chamber. Roots were collected immediately (control), 15 minutes, 30 minutes, 1, 2, 4, 8, and 24 hours after the LCO treatment. Roots were snap-frozen in liquid nitrogen, and roots from four plants were pooled for each of three biological replicates used in RNA sequencing. For each RNA extraction, roots from four plants were pooled and ground while keeping the sample frozen.

value: root

value: LCO treatment after 24 hour. Bio rep 3

value: Populus tremula x alba IRNA clone 717-1B4


title: WT BEAS-2B 3hr Replicate 3


title: CD41pos, WT1

value: CD41pos HSC

value: polyIC injection*4

value: 4 weeks post-injection


title: CD41neg, KO2

value: CD41ned HSC


title: CD41neg, WT4


title: 707 NIK KO IL4


title: 707 NIK KO NT


title: Spleen, CD44+ CD8+ T cells, rep 4

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

data_processing:
The adapter trimming was performed using fastq-mcf program (v1.05) and cutadapt (v2.5).
The unwanted sequences (mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences) were removed using Bowtie2 (v2.5.1).
Alignment was performed using STAR (v2.7.3a) aligner.
Raw read counts were estimated using cufflinks(v2.2.1).
Assembly: mm10
Supplementary files format and content: CounTable.xlsx: excel spreadsheet (.xlsx) of raw transcript counts
Supplementary files format and content: Normalized_log2.xlsx: excel spreadsheet (.xlsx) of FPKM values

source_name: spleen

extract_protocol:
RNA was harvested using Takara lysis solution per manufacturer's instructions by MedGenome, Inc.
RNA libraries for RNA-seq were prepared using Takara SMART-Seq v4 Ultra low Input RNA kit following manufacturer's protocols.

value: spleen

value: CD44+ CD8+ T cells


title: WT BEAS-2B 3hr Replicate 1

value: BEAS-2B Airway Epithelial Cells

value: Aspergillus fumigatus conidia


title: WT BEAS-2B 3hr Replicate 2


title: WT BEAS-2B 0hr Replicate 2


title: 24 hour rep 1

value: LCO treatment after 24 hour. Bio rep 1


title: Spleen, CD44+ CD8+ T cells, rep 1


title: 24 hour rep 2

value: LCO treatment after 24 hour. Bio rep 2


title: 700 WT NT

value: 12 weeks

value: Female

value: Bone marrow derrived macrophages

value: WT

value: PBS


title: Spleen, CD44+ CD8+ T cells, rep 3


title: 8 hour rep 2

value: root

value: LCO treatment after 8 hour. Bio rep 2


title: MUT SVE 3

city: Manchester

first: Jean-Michel

last: Fustin

state: England

address: Faculty of Biology, Medicine and Health, , Oxford road

department: Centre for Biological Timing

country: United Kingdom

institute: University of Manchester

data_processing:
Read trimming by Trimmomatic
QC with FastQC
aligment with HISAT2
Count and transcript assembly with Stringtie
Differential expression analysis with DESeq2
Assembly: GRCm39, vM27.annotations from GENCODE
Supplementary files format and content: DESeq2 output, tabular file containing normalised counts for all genes.

source_name: Suprachiasmatic nucleus

growth_protocol: All procedures were carried out under the UK Animals (Scientific Procedures) Act (1986) and approved by the University of Manchester Review Ethics Panel. Most experiments were conducted on adult male mice (>8 weeks of age) of two genotypes: C57BL/6 (wild-type, Vipr2+/+; Harlan, Blackthorn, UK) and transgenic mice lacking the VPAC2 receptor, Vipr2-/- (C57BL/6 background; initial breeding stock of Vipr2-/- donated by A. Harmar, University of Edinburgh). Mice were bred and maintained at 20–22 °C and ~40% humidity, with ad libitum access to food and water prior to and throughout experiments. Breeding rooms were maintained on a 12-h:12-h LD (LD 12:12) cycle.

extract_protocol:
Once entrained, animals in the SVE cohort were culled 2h after the time at which the wheel became available to exercise in (ZT14). For animals in the nSVE cohort, they were culled at one timepoint (CT14). The brain was removed, flash frozen on dry ice, and stored at -80 C. Brain sections of 20µm thickness were cut using a cryostat (Leica CM3050 S) onto PEN-membrane slides (Leica Biosystems, Germany) and then stored at -80 °C. Slides were then defrosted and to aid in identifying the SCN and its anatomical boundaries, sections were stained with 1% cresyl violet (Merck) in 70% ethanol. The SCN was identified and extracted on a laser-capture microscope (LCM) system (Leica DM6000 B) and stored in lysis buffer (Promega) prior to RNA extraction. RNA extraction was carried out with ReliaPrep Kit (Promage, UK).
Total RNA was checked using RNA 6000 Pico Kit (Agilent Technologies, USA) and amplified with Sense Total RNA-Seq Library Prep Kit (Lexogen, USA). RNA sequencing was done by paired-end sequencing on an Illumina HiSeq 4000 NGS platform (Genomic Technologies Core Facility, University of Manchester, UK)

treatment_protocol: At the start of behavioral screening, mice were placed for 14 days in LD12:12 and then the lights were turned off and the animals maintained in constant dark (DD) for the remainder of the experiment. In DD, mice were either allowed to free-run for the duration of the experiment (nSVE cohort) or were included in a SVE cohort. For this SVE cohort, animals free ran for 14 days and then their exercise in the running-wheel was restricted for 6h every 24h. Entrainment to SVE was defined as when the onset of drinking activity showed ~24h periodicity for 6-7 successive days. Vipr2-/- animals rapidly respond to SVE and show entrainment within 6-9 days (Hughes et al., 2021), whereas Vipr2+/+, mice took 35-40 days. Mice that did not entrain to SVE were not used in subsequent gene expression assessment and similarly, Vipr2-/- mice that were arrhythmic in the nSVE condition were also excluded.

value: SVE


title: 700 WT IL4

value: 20ng/mL IL-4 6hr


title: WT BEAS-2B 0hr Replicate 1


title: WT BEAS-2B 0hr Replicate 3


title: 4 hour rep 1

value: LCO treatment after 4 hour. Bio rep 1

value: Populus tremula x alba IRNA clone 717-1B4


title: Spleen, CD44+ CD8+ T cells, rep 2

value: spleen


title: 8 hour rep 3

value: LCO treatment after 8 hour. Bio rep 3


title: 4 hour rep 3

value: LCO treatment after 4 hour. Bio rep 3


title: Y48_2

city: Grand Forks

first: Lin

last: Yan

state: North Dakota

address: 2420 2nd Ave N

institute: USDA- Grand Forks Human Nutrition Research Center

description:
Y48_2
mRNA

data_processing:
Raw data (fastQ format) processed via fastp which clean data (clean reads) were obtained by removing reads containing adapter and pol-N- sequences. GC and phret scores were calculated at this time.
Clean paired-end reads were aligned to reference genome (obtained from NCBI) via STAR (version v2.5).
Quantification via HTSeq v0.6.1.
Differential Analysis via DESeq 2 (version v2_1.6.3, padju<0.05).
Enrichment Analysis via ClusterProfiler (version v2.4.3 with padj<0.05). Alternative splicing via rMATS (version v3.2.1 on default parameters) and Fusion gene analysis via STAR-Fusion (version v0.8.0 on default parameters).
Assembly: mm10
Supplementary files format and content: readcount_genename.xls: Raw counts of sequencing reads (before normalization) is provided in the matrix file. Column 1 provides the Ensembl ID, Column B-AQ provide the raw counts for each sample, columns AR-AY provide gene description (name, chromosomes, location, etc.)

source_name: Liver

extract_protocol:
Liver tissues were extracted via Qiazol method (RNeasy Tissue Lipid kit, Qiagen, MD USA). Concentration quantified via Spectrophometry 8000 (Thermofisher) and integrity on Qubit. Samples were sent off to Novogene USA for the complete analysis (mRNA methylation to total analysis of data).
Sequencing libraries were generated from 1 μg RNA per sample via NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. Library preparations were sequenced on an Illumina platform where paired-end reads were generated.

value: Liver

value: High-fat diet (HF)

value: Light phase (Zeitgeber time 0-12)

tag: time point


title: MUT SVE 1


title: Y48_3

description:
Y48_3
mRNA


title: 2 hour rep 3

value: LCO treatment after 2 hour. Bio rep 3


title: 8 hour rep 1

value: LCO treatment after 8 hour. Bio rep 1


title: 4 hour rep 2

value: LCO treatment after 4 hour. Bio rep 2


title: MUT SVE 2


title: LSKCD150+ HSCs, WT mice

description: 10X Genomic Chromium

value: bone marrow

value: RUNX1 WT


title: MUT non-SVE 3

value: non-SVE


title: Tumor, Kaede red+ CD44+ CD8+ T cells, rep 3

source_name: tumor retained (Kaede red+ in tumor)

value: tumor retained (Kaede red+ in tumor)

value: CD44+ CD8+ T cells


title: Y46_1

description:
Y46_1
mRNA

value: Female


title: Tumor, Kaede red+ CD44+ CD8+ T cells, rep 1


title: Y48_1

description:
Y48_1
mRNA


title: 2 hour rep 2

value: root

value: LCO treatment after 2 hour. Bio rep 2


title: Tumor, Kaede red+ CD44+ CD8+ T cells, rep 4


title: Y45_3

description:
Y45_3
mRNA


title: 2 hour rep 1

value: LCO treatment after 2 hour. Bio rep 1

value: Populus tremula x alba IRNA clone 717-1B4


title: MUT non-SVE 2


title: Egressed, Kaede red+ CD44+ CD8+ T cells, rep 4

source_name: egressed (Kaede red+ in tdLN)

value: egressed (Kaede red+ in tdLN)


title: Tumor, Kaede red+ CD44+ CD8+ T cells, rep 2


title: Y44_3

description:
Y44_3
mRNA

value: Liver


title: WT SVE 4

value: wildtype

value: SVE


title: 1 hour rep 2

value: LCO treatment after 1 hour. Bio rep 2


title: 1 hour rep 3

value: LCO treatment after 1 hour. Bio rep 3


title: Egressed, Kaede red+ CD44+ CD8+ T cells, rep 3


title: Y38_3

description:
Y38_3
mRNA

value: High-fat diet (HF)

value: Light phase (Zeitgeber time 0-12)


title: WT SVE 3


title: MUT non-SVE 1


title: Y39_1

description:
Y39_1
mRNA


title: 1 hour rep 1

value: LCO treatment after 1 hour. Bio rep 1


title: 30 min rep 3

value: LCO treatment after 30 min. Bio rep 3


title: Y41_2

description:
Y41_2
mRNA


title: 30 min rep 2

value: LCO treatment after 30 min. Bio rep 2


title: Egressed, Kaede red+ CD44+ CD8+ T cells, rep 1

value: CD44+ CD8+ T cells


title: WT SVE 2


title: W7_KO12

city: Atlanta

first: Saul

middle: Joseph

last: Karpen

state: GA

address: 1760 Haygood Dr NE

department: Pediatrics

institute: Emory School of Medicine

data_processing:
Fastp, STAR, HTseq, Cufflink, R/Deseq, and Novogene wrapped scripts.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software
FeatureCounts was used to count the read numbers mapped of each gene.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by Trimmed Mean of Mvalues (TMM) through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Gene id, normalized read counts for each Sample, log2FoldChange, pvalue, padj, gene name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, tf_family, readcount for each sample, fpkm for each sample - in that order.

source_name: tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: tissue

value: Hepatocytes, Cholangiocytes

value: LKO

value: female

value: NT

value: Week 7


title: Y37_2

description:
Y37_2
mRNA

value: Liver

value: Female


title: Egressed, Kaede red+ CD44+ CD8+ T cells, rep 2

value: egressed (Kaede red+ in tdLN)


title: WT SVE 1

value: wildtype

value: SVE


title: Y36_1

description:
Y36_1
mRNA

value: High-fat diet (HF)

value: Dark phase (Zeitgeber time 12-24)


title: Y35_3

description:
Y35_3
mRNA


title: W7_KO4


title: WT non-SVE 3

value: non-SVE


title: 15 min rep 2

value: root

value: LCO treatment after 15 min. Bio rep 2

value: Populus tremula x alba IRNA clone 717-1B4


title: Y32_3

description:
Y32_3
mRNA


title: W7_KO3

value: tissue


title: Y33_2

description:
Y33_2
mRNA


title: W7_CTL5

value: Hepatocytes, Cholangiocytes

value: Fl/Fl


title: W7_KO13

value: LKO

value: female


title: 709 NIK KO IL4

value: 12 weeks

value: Bone marrow derrived macrophages

value: NIK KO

value: 20ng/mL IL-4 6hr


title: WT non-SVE 2

value: wildtype


title: WT non-SVE 1


title: Glioblastoma, high-functional connectivity, patient 11748

city: San Francisco

first: Abrar

last: Choudhury

state: California

institute: University of California, San Francisco

description:
RED_11748
gbm_tpm.csv

data_processing:
Standard Illumina software was used for basecalling
Sequenced reads were trimmed using Trimmomatic, then mapped to hg38 transcriptome using HISAT2 2.1.0
Exon level count data were extracted from the mapped reads using featureCounts
Transcripts per million (TPM) were calculated from the count data
Assembly: hg38
Supplementary files format and content: Matrix table with TPMs for every gene and every sample

source_name: glioblastoma

extract_protocol:
RNA was extracted from the glioblatoma samples using the Qiagen RNeasy Plus Universal Kit (CAT# 73404)
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded RNA Library Prep Kit v2 (CAT# RS-122-2001)

value: glioblastoma

tag: functional connectivity

value: high

value: M


title: priB_MicroC_WT

city: Vienna

first: Maximilian

last: von der Linde

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

institute: Institute of Molecular Pathology

description: Micro-C

data_processing:
Library strategy: Micro-C
Micro-C
Raw sequening reads were processed and aligned to the mm9 reference with the distiller-nf pipeline (https://github.com/open2c/distiller-nf) using default parameters.
In brief, reads were split into smaller chunks, quality and adapter trimmed using fastp and subsequently aligned with the Burrows Wheeler aligner.
Split BAM files were sorted by position, merged, deduplicated with pairtools (https://github.com/open2c/pairtools).
Contact maps in different resolutions were then computed from generated pairs files using cooler commandline tools and balanced using iterative correction.
Assembly: NCBI mm9
Supplementary files format and content: mcool

source_name: primary B-cells

growth_protocol: Complete RPMI with LPS and IL4

extract_protocol:
Performed exactly as in Hsieh et al. (Moleular Cell 2020)
Performed exactly as in Hsieh et al. (Moleular Cell 2020)

treatment_protocol: 4-hydroxy tamoxifen for 32h

value: Spt5 depleted


title: Y30_3

description:
Y30_3
mRNA

value: Liver

value: Female

value: High-fat diet (HF)

value: Dark phase (Zeitgeber time 12-24)

tag: strain


title: WT non-SVE 4

value: non-SVE


title: 15 min rep 3

value: root

value: LCO treatment after 15 min. Bio rep 3

value: Populus tremula x alba IRNA clone 717-1B4


title: Glioblastoma, high-functional connectivity, patient 11956

description:
RED_11956
gbm_tpm.csv


title: 15 min rep 1

value: LCO treatment after 15 min. Bio rep 1


title: W7_CTL10

value: tissue

value: Hepatocytes, Cholangiocytes

value: Fl/Fl

value: male

value: NT

value: Week 7


title: Control rep 1

value: LCO control-time 0 bio rep 1


title: Control rep 2

value: LCO control-time 0 bio rep 2


title: W7_CTL9

value: female


title: Glioblastoma, high-functional connectivity, patient 12075

description:
RED_12075
gbm_tpm.csv

value: glioblastoma

value: high

value: F


title: Y32_1

description:
Y32_1
mRNA

value: Liver

value: Female

value: High-fat diet (HF)

value: Dark phase (Zeitgeber time 12-24)


title: Y28_3

description:
Y28_3
mRNA


title: Glioblastoma, low-functional connectivity, patient 12032

description:
BLUE_12032
gbm_tpm.csv

value: low


title: Y31_2

description:
Y31_2
mRNA


title: Control rep 3

value: root

value: LCO control-time 0 bio rep 3

value: Populus tremula x alba IRNA clone 717-1B4


title: Glioblastoma, low-functional connectivity, patient 12024

description:
BLUE_12024
gbm_tpm.csv

value: M


title: 30 min rep 1

value: LCO treatment after 30 min. Bio rep 1


title: Glioblastoma, low-functional connectivity, patient 11956

description:
BLUE_11956
gbm_tpm.csv


title: priB_MicroC_Spt5depleted

description: Micro-C

value: control


title: W7_CTL7

value: tissue

value: Hepatocytes, Cholangiocytes

value: Fl/Fl

value: NT

value: Week 7


title: Y25_3

description:
Y25_3
mRNA


title: Y27_3

description:
Y27_3
mRNA


title: priB_TriC_Spt5_IgG2acapture_dep_rep2

description: Tri-C

data_processing:
Library strategy: Tri-C
Tri-C
Demulitplexed reads were submitted to the CCseqBasicS5 pipeline with following options: bowtie2 alignment to NCBI mm9 , --tric, --flashbases 10
matrices were generated using the modified TriC_matrix_simple_MO.py script
Reads with alt least three interactions were extracted with TriCgetreads.py
Visualisation with pyplot in TriCplot.py
Find more information and scripts at https://github.com/PavriLab/tric
Assembly: mm9
Supplementary files format and content: Tab separated matrix showing normalized interaction counts

extract_protocol:
TriC was performed as described (Downes et al 2022 with modifications desribed in Costea, Schoeberl et al 2022). In short, 10x10^6 or 15x10^6 (0h) cells were crosslinked with 2% HCHO for 8 min at room temperature. After quenching with 0,133M glycine, cells were lysed and nuclei isolated. Next, nuclei were lysed followed by NlaIII digestion (overnight), T4-DNA-ligation (overnight), Proteinase K digestion (overnight) and genomic DNA extraction. DNA was sonicated on Covaris S2 sonicator.
TriC library was prepared of 3x2µg sonicated DNA using NEBUltraII and barcoding PCRs were performed using Nextflex unique dual index barcode sequences. For capture using reagents of the Roche HyperCap target enrichment kit and mouse Cot-1, 1-2µg of libraries were 2x (72h, 24h) hybridized to 2.9nM of individual biotinylated capture probes, followed by streptavidin pull down and PCR amplification using P5 and P7 (Illumina) primer sequences. Samples were multiplexed for sequencing on NextSeq or NovaSeq (Illumina) platforms

tag: capture probe

value: IgG2a capture

value: Spt5 62h activated, last 32h depleted with 4HT

tag: clone

value: clone 1

tag: replicate

value: replicate 2


title: priB_TriC_Spt5_IgG2acapture_dep_rep3

description: Tri-C

value: replicate 3


title: Y25_1

description:
Y25_1
mRNA

value: Liver

value: Female

value: High-fat diet (HF)

value: Dark phase (Zeitgeber time 12-24)


title: TmR_sh65_s1_S03: DLL1 KD2-repeat1

city: Philadelphia

first: Rumela

last: Chakrabarti

state: PA

address: 380 S University Ave

institute: University of Pennsylvania School of Veterinary Medicine

description: cell lines were made using lentivirus

data_processing:
Reads were counted against gencode v29 transcripts and summarized to the gene level with tximport in R
Genome_build: GRh38.p12
Genome_build: Gencode version 29
Supplementary_files_format_and_content: raw counts per gene, ensembl gene IDs, comma-separated values

source_name: tamoxifen resistant breast tumor cells

growth_protocol: Cells were grown in Iscoves media usings erum and Pen/Strep

extract_protocol:
Cells were trypsinized and then single cells were lysed using lysis buffer from Invitrogen RNA extration kit. Total RNA was isolated using standarad procedure following manufacture's protocol.
Library construction protocol was using standard protocol from Illumina

treatment_protocol: Cells were treated with trypsin for single cell isolation. DLL1 KD was made using lentivius mediated shRNAs from Sigma

value: tamoxifen resistant breast tumor cells

tag: condition


title: priB_TriC_Spt5_IgG2acapture_dep_rep1

description: Tri-C

value: replicate 1


title: Y24_2

description:
Y24_2
mRNA

value: Standard diet (LF)

value: Light phase (Zeitgeber time 0-12)


title: TmR_sh65_s2_S06: DLL1 KD2-repeat2

description: cell lines were made using lentivirus


title: priB_TriC_Spt5_IgG1poolcapture_dep_clone2_rep3

description: Tri-C

value: IgG1 pool capture

value: clone 2


title: TmR_sh64_s1_S02: DLL1 KD1-repeat1

description: cell lines were made using lentivirus


title: TmR_sh64_s2_S05: DLL1 KD1-repeat2

description: cell lines were made using lentivirus


title: priB_TriC_Spt5_IgG2acapture_ctrl_rep2

description: Tri-C

value: WT


title: Wild type, biological rep. 3

type: RNA

city: Nicosia

first: Constantinos

last: Deltas

state: Aglantzia

address: Palaios dromos Lefkosias Lemesou No.215/6

department: Biology

country: Cyprus

institute: University of Cyprus

description: Gene expression data from wild type samples

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hours at 45°C on GeneChip C.elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the AffyGeneChip Scanner 7G

data_processing:
Raw CEL files were background corrected, normalized and summarized using the RMA algorithm (PMID: 12582260) with Celegans_Ce_ENSG_21.0.0 (November 2016) as a custom Chip Description File (CDF) from the BrainArray project (PMID: 16284200). The Ensembl IDs were mapped to gene symbols using Ensembl BioMart and the Caenorhabditis elegans reference assembly WBcel235. Software versions: R v3.3.0, Bioconductor v3.3
RMA (Robust Multi-Array Average) signal intensity (PMID: 12582260)

label: biotin

organism: Caenorhabditis elegans

source_name: wild type Caenorhabditis elegans

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 150ng total RNA (GeneChip 3' IVT PLUS Reagent Manual, 2000, Affymetrix).

growth_protocol: Age-synchronized wild-type (N2) and dcap-1(tm3163) worms, grown at 20°C on OP50 bacteria in the presence of 10μg/ml 5-fluoro-2’-deoxyuridine (FUDR) were collected at the 9th day of adulthood.

extract_protocol: Total RNA was prepared from frozen worm pellets (200-300 worms per sample) of each sample using NucleoSpin RNA XS kit (Macherey-Nagel). Quality and quantity of RNA samples were determined using Nanodrop 2000 Spectrophotometer (Thermo Scientific).

treatment_protocol: Three populations of each strain were harvested from plates with M9 buffer, washed at least three times with M9 and their pellets were frozen at -80°C, until they were independently processed and analyzed.

value: whole worm

value: N2 wild type

value: 9 days

tag: developmental stage

value: adult

value: 10μg/ml FUDR


title: dcap-1 (reduction of function), biological rep. 2

description: Gene expression data from dcap-1 reduction of function samples

source_name: dcap-1 reduction of function Caenorhabditis elegans

tag: treatment


title: dcap-1 (reduction of function), biological rep. 3


title: priB_TriC_Spt5_IgG1poolcapture_dep_clone2_rep1

state: Vienna

description: Tri-C

growth_protocol: Complete RPMI medium with LPS and IL4 for activation

value: Spt5 62h activated, last 32h depleted with 4HT


title: TmR_plko_s1_S01: control-repeat1

description: cell lines were made using lentivirus

value: control


title: priB_TriC_Spt5_IgG2acapture_ctrl_rep1

description: Tri-C

value: IgG2a capture

value: clone 1


title: Y21_3

description:
Y21_3
mRNA

value: Liver

value: Female


title: priB_TriC_Spt5_IgG1poolcapture_dep_clone2_rep2

description: Tri-C

value: replicate 2


title: Y21_1

description:
Y21_1
mRNA

value: Standard diet (LF)


title: Y22_1

description:
Y22_1
mRNA

value: Light phase (Zeitgeber time 0-12)


title: Wild type, biological rep. 2


title: priB_TriC_Spt5_IgG1poolcapture_dep_clone1_rep4

description: Tri-C

value: IgG1 pool capture

value: replicate 4


title: dcap-1 (reduction of function), biological rep. 1


title: Wild type, biological rep. 1


title: Glioblastoma, low-functional connectivity, patient 11748

description:
BLUE_11748
gbm_tpm.csv

value: glioblastoma

value: low

value: M


title: Y17_1

description:
Y17_1
mRNA


title: Y23_3

description:
Y23_3
mRNA