title: human WBC, GB4030080 (iDNase-seq)


title: human WBC, GB4030079 (iDNase-seq)

status: Public on Aug 26 2022

type: SRA

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 10 Center Dr

department: Systems Biology Center

country: USA

institute: NHLBI

library_source: genomic

data_processing:
Basecalls performed
The raw fastq files are read and separated into 480 files corresponding to 96 pairs of cell barcodes over 5 replicates. The 480 pairs are shown in barcode_480.txt. A read is considered as belonging to one of the barcodes if the beginning of read 1 or read 2 contains the same pair of barcodes in the left and right column respectively.  After separting each set of fastq files into 480 files, some base pairs starting from 5' are trimmed and the remaining reads are mapped to the human genome using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 100 reads and a FRiP greater than 0.1. With these requirements, 4489 cells were obtained, and we were able to identify 218,042 DHSs. For each cell, we calculated the reads that were located within the DHS and stored the results in a matrix.
Genome_build: hg18
barcode_480.txt: two columns, the left column refers to a DNA barcode starting from the 5' end while the right column refers to a DNA barcode starting from the 3' end
peaks_218042_WBC.txt: first column is for chromsome, second column is for DHS start site, and third column is for DHS end site
iDNase_4489_cells_218042_peaks_counts_at_WBC.mtx: This file contains read count data for single cells in MatrixMarket format. Each row corresponds to a non-zero entry with the row, column, and then value specified. Reading the matrix results in a 218042 x 4489 matrix of peaks by cells where each element represents the number of reads located within a DHS site for some single cell.

molecule: genomic DNA

organism: Homo sapiens

source_name: WBC

extract_protocol:
DNase-seq human 1.25M 2-step crosslink human healthy T/B/NK/monocyte, final 0.1U/μl DNase digestion 37°C 5 minutes, T cell split #1-15 wells, B cell split #16-30 wells, NK cell split #31-45 wells, monocyte split #46-61 wells, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 20 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of PBMC suspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 10e6 cells per tube) at −80°C until use.

tag: cell type

value: WBC


title: Exp 2 DIO-NASH Chow Reversal w12 Rep 1

city: Hørsholm

first: Martin

middle: Rønn

last: Madsen

state: Please Select

address: Hørsholm Kongevej 11

department: Computation Biology

country: Denmark

institute: Gubra

library_source: transcriptomic

data_processing:
Reads were mapped to the GRCm38.p96 Ensembl mouse genome using STAR v.2.5.2a with default parameters.
Counts in protein coding genes was quantified using STAR and can be found in supplementary.
Assembly: GRCm38
Supplementary files format and content: .txt file of RPKM-normalized gene expression

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol: Illumina TruSeq Stranded mRNA Library Prep kit (#20020594, Illumina, San Diego, CA, USA)

tag: tissue

value: Liver

tag: treatment

value: DIO-NASH Chow Reversal w12

tag: weeks treatment


title: WT_Dark_0d_2

city: Shanghai

first: Moyang

last: Liu

address: dongchuan road 800

department: School of Agriculture and Biology

country: China

institute: Shanghai Jiao Tong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Assembly: TAIR10;IRGSP-1.0; SL3.0
Supplementary files format and content: tab-delimited text files include count for each Sample

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
10 μg/mg doxycycline treated and  control check leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

tag: genotype

value: WT

value: Dark

tag: time

value: Day 0


title: human WBC, GB4030078 (iDNase-seq)


title: WT_Dark_0d_1


title: WT_Dark_0d_3


title: Exp 2 Chow vehicle w12 Rep 5

value: Chow + vehicle w12


title: Exp 2 Chow vehicle w12 Rep 6


title: Exp 2 Chow vehicle w12 Rep 4


title: human WBC, GB4030076 (iDNase-seq)


title: human WBC, GB4030081 (iDNase-seq)


title: human WBC, GB4030082 (iDNase-seq)


title: human WBC, GB4030075 (iDNase-seq)


title: KO1

city: WuHan

first: Yugang

last: Li

address: shizishan street

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium tuberculosis H37Ra whole genome using bowtie2 v2-2.0.5
HTSeq was firstly applied to count the number of Fragments for each gene after bowtie2 comparison. Then the normalization was  completed with TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene is calculated by perl script.
Genome_build: Mycobacterium tuberculosis H37Ra
Supplementary_files_format_and_content: gene_expression.txt file includes FPKM and count values for each Sample.

organism: Mycobacterium tuberculosis H37Ra

source_name: strain

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen) following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNA Clean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mpbR-deleted


title: Exp 2 Chow vehicle w12 Rep 3


title: KO2


title: human WBC, GB4030100 (iDNase-seq)


title: human WBC, GB4030074 (iDNase-seq)


title: Exp 2 Chow vehicle w12 Rep 1


title: Exp 2 Chow vehicle w12 Rep 2


title: WT_Dark_7d_3

value: Day 7


title: human WBC, GB4030072 (iDNase-seq)


title: WT3

value: wild-type


title: WT1


title: KO3


title: pet3 [miRNA-seq]

city: Shenyang

first: Zhiyong

state: Liaoning Province

address: Dongling Road 120

institute: Shenyang Agriculral University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

organism: Brassica rapa

source_name: Chinese cabbage petiole

growth_protocol: Regular growth in the greenhouse

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: petiole

value: wild type

tag: molecule subtype

value: Small RNA


title: WT2


title: human WBC, GB4030071 (iDNase-seq)


title: human WBC, GB4030070 (iDNase-seq)


title: human WBC, GB4030069 (iDNase-seq)


title: pet1 [miRNA-seq]


title: human WBC, GB4030073 (iDNase-seq)


title: human WBC, GB4030067 (iDNase-seq)


title: pc-BMACs, rep1

city: Regensburg

first: Philipp

last: Beckhove

address: Franz-Josef-Strauss-Allee 11

country: Germany

institute: Regensburg Center for Interventional Immunology

description:
DR18s6_S5
PBMAC_R2

data_processing:
Sequenced reads were trimmed for adaptor sequences using skewer v0.2.2
Reads were mapped to mm10 whole genome using bowtie2 v2.3.3 with the –very-sensitive parameter and a maximum insert size of 2000 bp
Duplicate and unpaired reads were removed using the sambamba (Tarasov et al., 2015) ‘markdup’ command, and reads with mapping quality >30 and alignment to the nuclear genome were kept.
Peak calling for each sample was performed using HOMER v4.10 (Heinz et al., 2010) with the following approach: Two different peak sets were called, once we used the options ‘-style factor -fragmentLength 150 -size 250 -minDist 250 –L 4 –fdr 0.0001’ parameters, to identify highly robust small regions of open chromatin, and in a second approach we used the parameters ‘-region -fragmentLength 150 -size 150 -minDist 250 -L 4 -fdr 0.0001’ to identify larger regions of open chromatin. The two peak sets were then merged using the mergePeaks function of HOMER to create the peak set that was used for downstream analysis.
For visualization purposes only, coverage files from filtered bam files were produced using bedtools (Quinlan and Hall, 2010) genomeCoverageBed, each position was normalized by dividing to the total library size and multiplying by 106, followed by conversion to a bigwig using the bedGraphToBigWig command from the UCSC genome browser tools.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain bed files (peaks) and bigWig files (for genome browser visuaizations)

source_name: Lymphocytes

growth_protocol: Mice were housed at UKR central animal facility

extract_protocol:
Chromatin accessibility mapping on purified cell populations was performed using the ATAC-seq method as previously described (Buenrostro et al., 2013; Corces et al., 2017), with minor adaptations. Briefly, in each experiment 2,000 - 15,000 sorted cells were pelleted by centrifuging for 10 min at 4 °C at 500 x g. After centrifugation, the pellet was carefully lysed in 50 µl resuspension buffer supplemented with NP-40 (Sigma), Tween-20 and Digitonin (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 % NP-40, 0.1 % Tween-20, 0.01 % Digitonin) and incubated for 3 minutes on ice. Then, 1 ml of ice-cold resuspension buffer supplemented with Tween-20 was added, and the sample was centrifuged at 4 °C at 500 x g for 10 minutes. The supernatant was discarded, and the cell pellet was carefully resuspended in the transposition reaction (25 µl 2 x TD buffer (Illumina), 2.5 µl TDE1 (Illumina), 16.5 µl PBS, 5 µl nuclease-free water, 0.5 µl 1% Digitonin (Promega), 0.5 µl 10% Tween-20 (Sigma)) for 30 min at 37 °C on a shaker at 1000 rpm.
Following DNA purification with the Clean and Concentrator-5 kit (Zymo) eluting in 23 µl, 2 µl of the eluted DNA was used in a quantitative 10 µL PCR reaction (1.25 µM forward and reverse custom Nextera primers (Corces et al., 2017), 1x SYBR green final concentration) to estimate the optimum number of amplification cycles with the following program 72°C 5 min; 98°C 30 s; 25 cycles: 98°C 10 s, 63°C 30 s, 72°C 1 min; the final amplification of the library was carried out using the same PCR program and the number of cycles according to the Cq value of the qPCR. Library amplification using custom Nextera primers was followed by SPRI size selection with AmpureXP beads to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). The libraries were sequenced using the Illumina HiSeq3000/4000 or NextSeq platforms.

value: Balb/c

value: hematopoietic cell

tag: sorting markers


title: leaf1 [miRNA-seq]

source_name: Chinese cabbage leaf


title: human WBC, GB4030068 (iDNase-seq)


title: pc-BMACs, rep2

description:
DR18s10_S7
PBMAC_R3


title: bone marrow immature B cells, rep1

description:
DR18s5_S4
immatureBC_R2

value: B cell


title: bone marrow immature B cells, rep2

description:
DR18s13_S10
immatureBC_R4


title: sheep testis (6 months)

city: Lanzhou

first: Yao

middle: jing

last: Yue

address: NO.335 Jiangouyan, Qilihe District Lanzhou 730050, Gansu, P. R. C

department: Lanzhou Institute of Husbandry and Pharmaceutical Sciences,

institute: Chinese Academy of Agricultural Sciences

description: one sample from testis tissue

data_processing:
The cell Ranger software pipeline (version 3.1.0) provide by 10X genomics was used to demultplex cellular barcodes, map reads to the Genome
The Seruat package was used to screen the cells following preliminary quality control, while principal component analysis (PCA) for dimensionality reduction was used to analyze the similarity between qualified cells.
A mutual nearest neighbor (MNN)-clustering algorithm was used for clustering and classifying the cell types
Assembly: Ovis aries, Oar_rambouillet_v4.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

organism: Ovis aries

source_name: testis

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.25% trypsin/ethylenediaminetetraacetic acid (EDTA),Cells  were resuspended in DMEM/F-12 .
RNA libraries were prepared with Chromium Single cell 3 Reagent v3 Kits according to the manufactures protocol.

value: testis

tag: age

value: 6 month

tag: period

value: Sexual maturation


title: human WBC, GB4030065 (iDNase-seq)

value: WBC


title: Ythdc-RNAi HS RNA-seq rep3

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: RNA-seq

data_processing:
Paired-end FASTQs were trimmed using TrimGalore
Trimmed FASTQs were mapped using STAR-2.7.3a
Mapped BAM files were filtered for primary mapped reads in properly matching pairs using samtools
Count tables were produced for RNA-seq using an in-house R script utilizing the GenomicRanges summarizeOverlaps function
Differential expression tables were produced by DESeq2 from RNA-seq count tables
m6A-IP-seq was processed with MeTPeak for peak calling and RADAR for differential peak calling.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files for each condition represent log2(normalized m6A-IP counts/normalized input counts) and were produced using deepTools (bamCoverage to produce bw files from BAM files with --normalizeUsing CPM, and bwCompare using --operation log2

organism: Drosophila melanogaster

source_name: brain

growth_protocol: DaGal4> Control RNAi (BL35785),DaGal4> Mettl3 RNAi(BL80448), or DaGal4> Ythdc RNAi(BL34627) Drosophila crosses set up in 25 degree incubator. Male progeny collected 1-2 days post eclosion for treamtnet and RNA extraction.

extract_protocol:
For m6A-IP seq flies were flash frozen and head tissue was collected into cold RNAse free tubes. Total RNA was extracted from 200 Drosophila Heads per replicate using Trizol/ chloroform extraction. PolyA+ mRNA was obtained using NEBNext Poly(A) mRNA Magnetic Isolation Module. PolyA+ RNA was fragmented using the NEB Next Magnesium Fragmentation Module (NEB, E6150S) for 4 minutes at 95 °C for a 250 ng sample of polyA+ RNA, and RNA was repurified using the Zymo RNA clean & concentrator -5 kit (Zymo, R1013). 10% of the fragmented polyA+ RNA was saved as an input control for sequencing. M6A -immunoprecipitation was done using the EpiMark N6-Methyladenosine Enrichment kit protocol with some minor alteration. 30ul of protein G magnetic beads (NEB, #S1430) were washed and resuspended in IP buffer (150mM NaCl, 10mM Tris-HCL, 0.1% NP-40). 1.4ul of NEB m6A antibody (NEB, E1610S), or 4ul of synaptic systems antibody (SYS, 202003) was conjugated to protein G-magnetic beads (NEB, S1430S) for 2 hours at 4°C. Beads/ antibody were washed twice in IP buffer. ~1μg PolyA+ RNA was incubated with beads/antibody in IP buffer supplemented with 0.1% SUPERase-In RNase Inhibitor (Thermo Fisher; AM2696) for 2 hours at 4°C. After incubation, RNA/beads/antibody are washed twice in IP buffer, twice in low salt IP buffer (50mM NaCl, 10mM Tris-HCL, 0.1% NP-40), and twice in high salt IP buffer (500mM NaCl, 10mM Tris-HCL, 0.1% NP-40). RNA is eluted from beads with 25μl of RLT buffer twice and elution was pooled and concentrated using Zymo RNA clean and concentrator kit-5 (R1015). Libraries were made using SMARTer Stranded Total RNA-Seq Kit V2 without rRNA depletion (takarabio, 634411) for IPed and input RNA, and sequenced using illumina HiSeq with 40M paired end reads (2x150bp). Library preparation and sequencing was done by Admera Health. Three biological replicates per genotype and condition were done with NEB m6A antibody, and two biological replicates were done with Synaptic Systems m6A antibody. Total RNA was extracted from brains using trizol/chloroform and Zymo RNA clean and concentrator kit-5 (R1015). The RNA-seq libraries from brains were prepared using the Tru-seq stranded mRNA library prep. Library preparation and sequencing was done by Admera Health, and sequenced using illumina HiSeq with 40M paired end reads (2x150bp). Three biological replicates were done for each experimental timepoint, condition, and genotype. Technical repeats and repeat additional biological replicates were done as indicated.
Libraries were made using SMARTer Stranded Total RNA-Seq Kit V2 without rRNA depletion (takarabio, 634411) for IPed and input RNA, The RNA-seq libraries from brains were prepared using the Tru-seq stranded mRNA library prep. Both m6A-IP and RNa-seq were sequenced using illumina HiSeq with 40M paired end reads (2x150bp).

treatment_protocol: Control RNAi, Mettl3 RNAi, or Ythdc RNAi male progeny were collected and anesthetized. Tissue was collected in basal conditions, immediately post Heat stress (HS), or HS and recovered for 6hrs or 24hrs. For HS, flies were placed into clear vials (20 flies per vial) and were HS for 30 minutes at 38.5°C. For HS recovery, flies were HS for 30 minutes at 38.5°C and allowed to recover on regular food in the 25°C incubator for 6hr or 24 hrs.

tag: heat shock condition

value: 30 minute heat shock

value: Ythdc RNAi


title: Ythdc-RNAi HS RNA-seq rep2

description: RNA-seq


title: human WBC, GB4030064 (iDNase-seq)


title: Bone marrow plasma cells, rep2

description:
DR18s16_S12
classicalPC_R4

value: plasma cell


title: human WBC, GB4030063 (iDNase-seq)


title: Bone marrow plasma cells, rep1

description:
DR18s12_S9
classicalPC_R3


title: Ythdc-RNAi HS RNA-seq rep1

description: RNA-seq


title: pet2 [miRNA-seq]


title: human WBC, GB4030062 (iDNase-seq)


title: Host tTregs, rep2

description:
tTreg_R2_ATACseq_omniATAC1_10000_illuminaTn5_DR31s2_S2
tTreg_R2_ATACseq_omniATAC1_10000_illuminaTn5_DR31s2_S2

value: T cell


title: Host tTregs, rep1

description:
tTreg_R1_ATACseq_omniATAC1_10124_illuminaTn5_DR31s1_S1
tTreg_R1_ATACseq_omniATAC1_10124_illuminaTn5_DR31s1_S1


title: Ythdc-RNAi basal RNA-seq rep3

description: RNA-seq

value: basal


title: leaf3 [miRNA-seq]

value: leaf


title: human WBC, GB4030061 (iDNase-seq)


title: human WBC, GB4030066 (iDNase-seq)


title: leaf2 [miRNA-seq]


title: Ythdc-RNAi basal RNA-seq rep1

description: RNA-seq


title: human WBC, GB4030060 (iDNase-seq)


title: Host pTregs, rep2

description:
pTreg_R2_ATACseq_omniATAC1_10000_illuminaTn5_DR31s4_S4
pTreg_R2_ATACseq_omniATAC1_10000_illuminaTn5_DR31s4_S4


title: human WBC, GB4030077 (iDNase-seq)


title: in vitro-induced Tregs, rep1

description:
iTreg_R1_CD45-2Pos_CD25Pos_LAPPos_WTBalbc
iTreg_ATACseq_omniATAC1_50000_illuminaTn5_R1


title: in vitro-induced Tregs, rep2

description:
iTreg_R2_CD45-2Pos_CD25Pos_LAPPos_WTBalbc
iTreg_ATACseq_omniATAC1_50000_illuminaTn5_R2


title: control-RNAi HS RNA-seq rep8

description: RNA-seq; control matched with Ythdc RNAi samples

value: control RNAi


title: Ythdc-RNAi basal RNA-seq rep2

description: RNA-seq


title: control-RNAi HS RNA-seq rep9


title: human WBC, GB4030058 (iDNase-seq)


title: human WBC, GB4030057 (iDNase-seq)


title: control-RNAi HS RNA-seq rep7


title: Host pTregs, rep1

description:
pTreg_R1_ATACseq_omniATAC1_9859_illuminaTn5_DR31s3_S3
pTreg_R1_ATACseq_omniATAC1_9859_illuminaTn5_DR31s3_S3


title: Host WT conventional T cells, rep2

description:
HTconv_R3_CD45-1Pos_CD25Neg_Aire-HCO
HTconv_ATACseq_omniATAC1_50000_illuminaTn5_R3_CD45-1plusCD45-2minusCD3plusCD4plusCD25minus_AireminusHCO_BW13s6_S4


title: human WBC, GB4030055 (iDNase-seq)


title: human WBC, GB4030059 (iDNase-seq)


title: control-RNAi basal RNA-seq rep8


title: human WBC, GB4030056 (iDNase-seq)


title: control-RNAi basal RNA-seq rep7


title: Donor 6.5TCR T cells which were converted to Tregs, rep2

description:
B-Treg_R3_CD45-2Pos_CD25PosLAPPos_6-5-TCR
BTreg_ATACseq_omniATAC1_16600_illuminaTn5_R3_CD45-1minusCD45-2plusCD3plusCD4plusCD25plusLAPplus_6-5minusTCR_BW13s9_S6


title: Donor 6.5TCR T cells which were converted to Tregs, rep1

description:
B-Treg_R2_CD45-2Pos_CD25PosLAPPos_6-5-TCR
BTreg_ATACseq_omniATAC1_17000_illuminaTn5_R2_CD45-1minusCD45-2plusCD3plusCD4plusCD25plusLAPplus_6-5minusTCR_BW13s8_S5


title: control-RNAi HS RNA-seq rep6

description:
RNA-seq
read_counts.txt.gz

growth_protocol: DaGal4> Control RNAi (BL35785) and DaGal4> Mettl3 RNAi(BL80448) Drosophila crosses set up in 25 degree incubator. Male progeny collected 1-2 days post eclosion for treatment and RNA extraction.

treatment_protocol: Control and Mettl3 RNAi male progeny were collected and anesthetized. Tissue was collected in basal conditions, immediately post Heat stress (HS), or HS and recovered for 6hrs or 24hrs. For HS, flies were placed into clear vials (20 flies per vial) and were HS for 30 minutes at 38.5°C. For HS recovery, flies were HS for 30 minutes at 38.5°C and allowed to recover on regular food in the 25°C incubator for 6hr or 24 hrs.

value: brain


title: human WBC, GB4030054 (iDNase-seq)


title: human WBC, GB4030053 (iDNase-seq)


title: Donor 6.5TCR T cells which were not converted to Tregs, rep2

description:
B-Tconv_R2_CD45-2Pos_CD25Neg_6-5-TCR
BTconv_ATACseq_omniATAC1_42000_illuminaTn5_R2_CD45-1minusCD45-2plusCD3plusCD4plusCD25minus_6-5minusTCR_BW13s11_S8


title: human WBC, GB4030052 (iDNase-seq)


title: Donor 6.5TCR T cells which were not converted to Tregs, rep1

description:
B-Tconv_R1_CD45-2Pos_CD25Neg_6-5-TCR
BTconv_ATACseq_omniATAC1_43000_illuminaTn5_R1_CD45-1minusCD45-2plusCD3plusCD4plusCD25minus_6-5minusTCR_BW13s10_S7


title: control-RNAi HS RNA-seq rep5

description:
RNA-seq
read_counts.txt.gz


title: control-RNAi HS RNA-seq rep4

description:
RNA-seq
read_counts.txt.gz


title: human WBC, GB4030051 (iDNase-seq)


title: control-RNAi basal RNA-seq rep9


title: control-RNAi basal RNA-seq rep6

description:
RNA-seq
read_counts.txt.gz


title: Primary adult fibroblasts [IR_rna]

city: Ann Arbor

first: Gabrielle

last: Dotson

state: Michigan

address: 1600 Huron Parkway

institute: University of Michigan

data_processing:
Reads which passed Q-score filtering (--min_qscore 7, 4.56 million reads) after base calling on the Oxford Nanopore GridION (Guppy, version 4.0.11) were used as input for the Pore-C-Snakemake pipeline (https://github.com/nanoporetech/Pore-C-Snakemake, commit 6b2f762).  The pipeline maps multi-way contacts to a reference genome and stores the hyperedge data in a variety of formats.
The reference genome used for mapping was GRCh38.p13. Each of the four sequencing runs were assigned a sequencing run label and then concatenated. The combined pipeline outputs were used as standard inputs for all downstream analysis.
Assembly: GRCh38.p13
Supplementary files format and content: For processed Pore-C data, the file format is a MATLAB table containing genomic positions of contacting DNA loci and their unique read ID
Supplementary files format and content: For processed RNA-seq data, the file format is a MATLAB table containing normalized read counts for genes genome-wide in each sample replicate

source_name: adult fibroblasts

growth_protocol: Primary human adult dermal fibroblasts were obtained from a donor and were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10\% fetal bovine serum (FBS), 1X Glutamax (Thermo Fisher Scientific Cat no. 35050061) and 1X nonessential amino acid (Thermo Fisher Scientific Cat no. 11140050).

extract_protocol:
Proximity ligated sample was treated with  100uL Proteinase K (NEB P8107S-800U/ml), 100uL 10% SDS (Invitrogen Cat no. 15553-035) and 500uL 20% v/v Tween-20 (Sigma Aldrich Cat no. P1379) in a total volume of 2000uL with nuclease-free water. The mixture was incubated in a thermal block at 56C for 18 hours. In order to purify DNA, the sample was transferred to a 15mL centrifuge tube, rinsing the original tube with a further 200uL of nuclease-free water to collect any residual sample, bringing the total sample volume to 2.2mL. DNA was then purified from the sample using a standard phenol chloroform extraction and ethanol precipitation.
Purified DNA was Solid Phase Reversible Immobilization (SPRI) size selected before library preparation with a bead ratio of 0.48X for fragments >1.5 kb. The >1.5 kb products were prepared for sequencing using the protocol provided by Oxford Nanopore Technologies. In brief, 1ug of genomic DNA input was used to generate a sequencing library according to the protocol provided for the SQK-LSK109 kit (Oxford Nanopore Technologies, Oxford Science Park, UK, version GDE_9063_v109_revU_14Aug2019). After the DNA repair, end prep, and adapter ligation steps, SPRI select bead suspension (Cat No. B23318, Beckman Coulter Life Sciences, Indianapolis, IN, USA) was used to remove short fragments and free adapters. A bead ratio of 1X was used for DNA repair and end prep while a bead ratio of 0.4X was used for the adapter ligation step. Qubit dsDNA assay (ThermoFisher Scientific, Waltham, MA, USA) was used to quantify DNA and 300-400 ng of DNA library was loaded onto a GridION flow cell (version R9, Flo-MIN 106D). For adult fibroblasts, 4 sequencing runs were conducted generating a total of 6.25 million reads (referred to as V1-V4). For neonatal fibroblasts, 4 sequencing runs were conducted generating a total of 11.85 million reads.

treatment_protocol: Protocols for cross-linking were based on Deshpande et al. 2.5 million cells were washed three times in chilled 1X phosphate buffered saline (PBS) in a 50mL centrifuge tube, pelleted by centrifugation at 500 x g for 5 min at 4C between each wash. Cells were resuspended in 10mL room temperature 1X PBS 1% formaldehyde (Fisher Scientific Cat no. BP531-500) by gently pipetting with a wide bore tip, then incubated at room temperature for 10 min. To quench the cross-linking reaction 527uL of 2.5 M glycine was added to achieve a final concentration of 1% w/v or 125 mM in 10.5 mL. Cells were incubated for 5 min at room temperature followed by 10 min on ice. The cross-linked cells were pelleted by centrifugation at 500 x g for 5 min at 4C.

value: adult fibroblasts

value: WT


title: human WBC, GB4030050 (iDNase-seq)


title: Neonatal fibroblast cell lin [BJ_porec]

data_processing:
Library strategy: Pore-C
Reads which passed Q-score filtering (--min_qscore 7, 4.56 million reads) after base calling on the Oxford Nanopore GridION (Guppy, version 4.0.11) were used as input for the Pore-C-Snakemake pipeline (https://github.com/nanoporetech/Pore-C-Snakemake, commit 6b2f762).  The pipeline maps multi-way contacts to a reference genome and stores the hyperedge data in a variety of formats.
The reference genome used for mapping was GRCh38.p13. Each of the four sequencing runs were assigned a sequencing run label and then concatenated. The combined pipeline outputs were used as standard inputs for all downstream analysis.
Assembly: GRCh38.p13
Supplementary files format and content: For processed Pore-C data, the file format is a MATLAB table containing genomic positions of contacting DNA loci and their unique read ID
Supplementary files format and content: For processed RNA-seq data, the file format is a MATLAB table containing normalized read counts for genes genome-wide in each sample replicate

source_name: BJ

tag: cell line

value: BJ

value: neonatal fibroblasts


title: Host WT conventional T cells, rep1

description:
HTconv_R2_CD45-1Pos_CD25Neg_Aire-HCO
HTconv_ATACseq_omniATAC1_50000_illuminaTn5_R2_CD45-1plusCD45-2minusCD3plusCD4plusCD25minus_AireminusHCO_BW13s5_S3

value: Balb/c


title: Primary adult fibroblasts [IR_porec]


title: control-RNAi basal RNA-seq rep5

description:
RNA-seq
read_counts.txt.gz


title: PO18 elevated temperature

city: Nathan

first: Tessa

middle: M

last: Page

state: QLD

address: 170 Kessels Road

department: Science and Environment

country: Australia

institute: Griffith University

data_processing:
Customised sequencing was performed on a single lane of an Illumina NovaSeq 6000, sequencing 26 bp on read 1, and 100 bp on read 2.
Raw sequence data were processed using Illumina BCL2FASTQ.
Quality control was performed with FastQC.
CEL-Seq-pipeline (https://github.com/yanailab/CEL-Seq-pipeline) for demultiplexing and mapping.
Assembly: Reference transcriptomes were created using transcriptomes for P. onkodes and S. durum (NCBI BioProject PRJNA518156, accession numbers GHIN00000000.1 and GHIO00000000.1 for S. cf. durum and P. cf. onkodes, respectively).
Supplementary files format and content: csv matrix of counts data for Porolithon onkodes
Supplementary files format and content: csv matrix of counts data for Sporolithon durum

organism: Porolithon cf. onkodes

source_name: pigmented tissue

growth_protocol: Coralline algae were cultured for three months in flow through aquarium where temperature and pH were altered.

extract_protocol:
Fragments of CCA were thoroughly cleaned prior to sampling for molecular analysis under a microscope and all epiphytes, as far as possible, were removed. CCA were rinsed with filtered seawater and RNAlater® and then blotted with a kimwipe to remove bacterial film. RNA was extracted following a modified TRIzol protocol.
cDNA synthesis, library preparation, and sequencing followed the single-cell sequencing (CEL-Seq2) protocol detailed in Hashimonshony et al. 2016

treatment_protocol: Fragments of CCA (20 per species) were divided across four treatments [“control” (unmanipulated seawater conditions, 27.2 ºC, 8.0 pH/450 µatm pCO2), “T” (elevated temperature and ambient pH, 29.5 ºC, 8.0 pH/450 µatm pCO2), “pH” (reduced pH and ambient temperature, 27.2 ºC, 7.7 pH/1000 µatm pCO2), or “T+pH” (elevated temperature and reduced pH, 29.5 ºC, 7.7 pH/1000 µatm pCO2)] with five biological replicates (n = 5) per treatment for a duration of three months.

value: pigmented tissue

value: elevated temperature


title: PO17 control

value: control


title: PO19 elevated temperature + reduced pH

value: elevated temperature + reduced pH


title: human WBC, GB4030047 (iDNase-seq)

value: WBC


title: Mettl3-RNAi HS RNA-seq rep5

description:
RNA-seq
read_counts.txt.gz

value: 30 minute heat shock

value: Mettl3 RNAi


title: Mettl3-RNAi HS RNA-seq rep6

description:
RNA-seq
read_counts.txt.gz


title: human WBC, GB4030044 (iDNase-seq)


title: PO16 control


title: Mettl3-RNAi HS RNA-seq rep4

description:
RNA-seq
read_counts.txt.gz


title: control-RNAi basal RNA-seq rep4

description:
RNA-seq
read_counts.txt.gz


title: Mettl3-RNAi basal RNA-seq rep5

description:
RNA-seq
read_counts.txt.gz


title: human WBC, GB4030043 (iDNase-seq)


title: PO15 elevated temperature + reduced pH


title: PO14 reduced pH

value: reduced pH


title: Mettl3-RNAi basal RNA-seq rep4

description:
RNA-seq
read_counts.txt.gz

value: basal


title: human WBC, GB4030042 (iDNase-seq)


title: PO13 control


title: human WBC, GB4030049 (iDNase-seq)


title: human WBC, GB4030048 (iDNase-seq)


title: human WBC, GB4030041 (iDNase-seq)


title: PO12 elevated temperature + reduced pH


title: human WBC, GB4030046 (iDNase-seq)


title: human WBC, GB4030040 (iDNase-seq)


title: PO11 reduced pH


title: control-RNAi HS RNA-seq rep3

description:
RNA-seq
read_counts.txt.gz


title: control-RNAi HS RNA-seq rep2

description:
RNA-seq
read_counts.txt.gz


title: control-RNAi HS RNA-seq rep1

description:
RNA-seq
read_counts.txt.gz


title: PO10 control


title: human WBC, GB4030045 (iDNase-seq)


title: human WBC, GB4030038 (iDNase-seq)


title: Mettl3-RNAi basal RNA-seq rep6

description:
RNA-seq
read_counts.txt.gz


title: control-RNAi HS+6hr_rec RNA-seq rep2

description:
RNA-seq
read_counts.txt.gz

value: 30 minute heat shock + 6h recovery

tag: recovery timepoint

value: 6 h


title: control-RNAi HS+6hr_rec RNA-seq rep1

description:
RNA-seq
read_counts.txt.gz

value: control RNAi

value: brain


title: human WBC, GB4030037 (iDNase-seq)


title: human WBC, GB4030036 (iDNase-seq)


title: control-RNAi HS+24hr_rec RNA-seq rep2

description:
RNA-seq
read_counts.txt.gz

value: 30 minute heat shock + 24h recovery


title: human WBC, GB4030035 (iDNase-seq)


title: control-RNAi HS+24hr_rec RNA-seq rep3

description:
RNA-seq
read_counts.txt.gz


title: human WBC, GB4030034 (iDNase-seq)


title: control-RNAi HS+24hr_rec RNA-seq rep1

description:
RNA-seq
read_counts.txt.gz


title: human WBC, GB4030033 (iDNase-seq)


title: PO7 elevated temperature + reduced pH


title: PO9 reduced pH


title: PO5 reduced pH


title: PO8 elevated temperature


title: PO4 control


title: PO6 elevated temperature + reduced pH


title: human WBC, GB4030039 (iDNase-seq)


title: human WBC, GB4030032 (iDNase-seq)


title: human WBC, GB4030031 (iDNase-seq)


title: PO3 reduced pH


title: control-RNAi basal RNA-seq rep3

description:
RNA-seq
read_counts.txt.gz


title: control-RNAi basal RNA-seq rep2

description:
RNA-seq
read_counts.txt.gz


title: control-RNAi basal RNA-seq rep1

description:
RNA-seq
read_counts.txt.gz


title: PO1 elevated temperature


title: human WBC, GB4030029 (iDNase-seq)


title: human WBC, GB4030030 (iDNase-seq)


title: IM3

city: Bengbu

first: Qian

last: Kaiqiang

state: --- Select One ---

address: China

department: School of Life Sciences

institute: Bengbu Medical College

description: biol rep 3

data_processing:
The image data measured by the high-throughput sequencer are convertedintosequence data (reads) by CASAVA base recognition
Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the reference genome usingHisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: human peripheral blood

growth_protocol: THP1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS)  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIZOL (Qiagen). 1.5ng/μl of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared  following manufacturer's protocols.

treatment_protocol: After 72 h of PMA induction, the follow-up experiments were continued.

value: human peripheral blood

value: human monocytic leukemia

value: WT

value: PMA induction ,H37Ra infection for 4h, Isoniazid and 200uM Mn2+ treatment for 12h


title: PO2 elevated temperature

value: pigmented tissue

value: elevated temperature


title: Mettl3-RNAi HS RNA-seq rep2

description:
RNA-seq
read_counts.txt.gz


title: Mettl3-RNAi HS RNA-seq rep3

description:
RNA-seq
read_counts.txt.gz


title: IM2

description: biol rep 2


title: human WBC, GB4030028 (iDNase-seq)


title: IM1

description: biol rep 1


title: Mettl3-RNAi HS+6hr_rec RNA-seq rep3

description:
RNA-seq
read_counts.txt.gz


title: Mettl3-RNAi HS RNA-seq rep1

description:
RNA-seq
read_counts.txt.gz


title: control-RNAi HS m6A-IP SYS rep2

description:
m6A-IP-seq
control_RNAi.HS.sys.log2_m6A_input.bw
read_counts.txt.gz

source_name: head

tag: ip antibody

value: SYS

value: head


title: control-RNAi HS m6A-IP SYS rep1

value: 30 minute heat shock


title: human WBC, GB4030026 (iDNase-seq)

value: WBC


title: human WBC, GB4030027 (iDNase-seq)


title: control-RNAi HS input SYS rep2

description:
input for m6A-IP-seq
control_RNAi.HS.sys.log2_m6A_input.bw
read_counts.txt.gz


title: INH3

description: biol rep 3

value: PMA induction,H37Ra infection for 4h and Isoniazid treatment for 12h


title: Mettl3-RNAi HS+6hr_rec RNA-seq rep1

description:
RNA-seq
read_counts.txt.gz

value: Mettl3 RNAi


title: human WBC, GB4030024 (iDNase-seq)


title: Mettl3-RNAi HS+6hr_rec RNA-seq rep2

description:
RNA-seq
read_counts.txt.gz

value: 30 minute heat shock + 6h recovery


title: human WBC, GB4030025 (iDNase-seq)


title: INH2

description: biol rep 2


title: control-RNAi HS m6A-IP NEB rep2

description:
m6A-IP-seq
control_RNAi.HS.neb.log2_m6A_input.bw
read_counts.txt.gz

value: NEB


title: RM3

description: biol rep 3

value: PMA induction ,H37Ra infection for 4h and 200uM Mn2+ treatment for 12h


title: control-RNAi HS m6A-IP NEB rep3

value: control RNAi


title: human WBC, GB4030022 (iDNase-seq)


title: human WBC, GB4030023 (iDNase-seq)


title: Mettl3-RNAi basal RNA-seq rep3

description:
RNA-seq
read_counts.txt.gz

value: basal

value: brain


title: RM1

description: biol rep 1

value: human peripheral blood

value: human monocytic leukemia


title: Mettl3-RNAi HS+24hr_rec RNA-seq rep1

description:
RNA-seq
read_counts.txt.gz

value: 30 minute heat shock + 24h recovery


title: RM2

description: biol rep 2

value: WT


title: control-RNAi HS input NEB rep3

description:
input for m6A-IP-seq
control_RNAi.HS.neb.log2_m6A_input.bw
read_counts.txt.gz


title: control-RNAi HS m6A-IP NEB rep1


title: human WBC, GB4030020 (iDNase-seq)


title: control-RNAi HS input SYS rep1


title: human WBC, GB4030021 (iDNase-seq)


title: Mettl3-RNAi basal RNA-seq rep2

description:
RNA-seq
read_counts.txt.gz


title: Mettl3-RNAi HS+24hr_rec RNA-seq rep3

description:
RNA-seq
read_counts.txt.gz


title: INH1

description: biol rep 1


title: Mettl3-RNAi basal RNA-seq rep1

description:
RNA-seq
read_counts.txt.gz


title: human WBC, GB4030019 (iDNase-seq)


title: Ra2

description: biol rep 2

value: PMA induction and H37Ra infection for 4h


title: 73759

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description: High-plane of nutrition

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: ARS1.2
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: Testes

growth_protocol: Holstein-Friesian bull calves were fed differentially either a High plane of nutrition (n=15) or a Moderate plane of nutrition (n=15)  from 2-12 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.0 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
RNA was  precipitated and purified from testes samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates. The Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates.

tag: diet

value: Moderate

value: Testes

tag: breed

value: Holstein-Friesian


title: human WBC, GB4030018 (iDNase-seq)

tag: cell type

value: WBC


title: control-RNAi basal m6A-IP SYS rep1

description:
m6A-IP-seq
control_RNAi.basal.sys.log2_m6A_input.bw
read_counts.txt.gz

value: SYS

tag: tissue

value: head


title: control-RNAi basal m6A-IP SYS rep2


title: Ra3

description: biol rep 3

tag: treatment


title: Mettl3-RNAi HS+24hr_rec RNA-seq rep2

description:
RNA-seq
read_counts.txt.gz

value: Mettl3 RNAi


title: control-RNAi HS input NEB rep2

value: 30 minute heat shock


title: control-RNAi HS input NEB rep1


title: 61965

description: High-plane of nutrition


title: 37840

description: Moderate-plane of nutrition

value: High


title: human WBC, GB4030017 (iDNase-seq)


title: Blank3

description: biol rep 3

value: PMA induction


title: control-RNAi basal input SYS rep2

description:
input for m6A-IP-seq
control_RNAi.basal.sys.log2_m6A_input.bw
read_counts.txt.gz

value: basal

value: control RNAi


title: Ra1

description: biol rep 1

value: human peripheral blood


title: control-RNAi basal m6A-IP NEB rep3

description:
m6A-IP-seq
control_RNAi.basal.neb.log2_m6A_input.bw
read_counts.txt.gz

value: NEB


title: Blank2

description: biol rep 2

value: human monocytic leukemia


title: human WBC, GB4030015 (iDNase-seq)


title: control-RNAi basal input SYS rep1


title: human WBC, GB4030016 (iDNase-seq)


title: human WBC, GB4030014 (iDNase-seq)


title: Blank1

description: biol rep 1

value: WT


title: control-RNAi basal m6A-IP NEB rep2


title: 27848

description: Moderate-plane of nutrition


title: 37824

description: High-plane of nutrition


title: control-RNAi basal m6A-IP NEB rep1


title: Jlat 8.4 Hi-C (+TNF-alpha, GFP positive)

city: La Jolla

first: Jesse

middle: R

last: Dixon

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

data_processing:
Hi-C reads were aligned to the hg38 reference genome using BWA and processed with custom perl scripts (available from https://github.com/dixonlab/HiC_alignment_basic_scripts).
Processed Hi-C files were generated by first converting aligned bam files to contact files using custom perl scripts (available from https://github.com/dixonlab/HiC_alignment_basic_scripts). *.hic files were generated using juicer.
Genome_build: b38
Supplementary_files_format_and_content: *hic files

source_name: Jlat 8.4 cell line

growth_protocol: Cells were cultured in RPMI-1640 with 10% FBS and 2mM L-glutamine in a 37C incubator with 5% CO2

extract_protocol:
For Hi-C, cells were fixed with 1% formaldehyde for 10 minutes at room temperture, quenched with 0.2M Glycine for 5 minutes. After fixation and quenching, cells were pelleted, washed 1X with DPBS, pelleted again, and frozen on dry ice. Samples were stored in -80C until further processing.
In situ Hi-C was performed accoring to Rao et al. Cell 2014 using the MboI restriction enzyme. Libraries were sequenced on the Novoseq 6000 platform.

treatment_protocol: HIV latency reversal was achieved using 10 ng/uL of TNF-alpha simulation for 24 hours

value: Jlat 8.4 cell line

tag: experiment type

value: MboI in situ Hi-C

value: TNF-alpha


title: 47874

description: High-plane of nutrition

value: Moderate

value: Testes

value: Holstein-Friesian


title: human WBC, GB4030012 (iDNase-seq)

value: WBC


title: Jlat 10.6 Hi-C (+TNF-alpha, GFP negative)

source_name: Jlat 10.6 cell line

value: Jlat 10.6 cell line


title: 31979

description: Moderate-plane of nutrition


title: 61973

description: High-plane of nutrition


title: control-RNAi basal input NEB rep2

description:
input for m6A-IP-seq
control_RNAi.basal.neb.log2_m6A_input.bw
read_counts.txt.gz

tag: genotype

value: head


title: Jlat 10.6 Hi-C (+TNF-alpha, GFP positive)


title: control-RNAi basal input NEB rep3


title: Jurkat Hi-C (+TNF-alpha)

source_name: Jurkat cell line

value: Jurkat


title: human WBC, GB4030013 (iDNase-seq)

source_name: WBC


title: 37865

description: High-plane of nutrition


title: human WBC, GB4030011 (iDNase-seq)


title: 81983

description: Moderate-plane of nutrition

value: High


title: Jlat 8.4 Hi-C (+TNF-alpha, GFP negative)


title: control-RNAi basal input NEB rep1

value: basal


title: human WBC, GB4030010 (iDNase-seq)


title: human WBC, GB4030008 (iDNase-seq)


title: Jurkat Hi-C (control)

value: Control


title: 27864

description: Moderate-plane of nutrition


title: µCP-EB D7 - Donor 2

city: Aachen

first: Mohamed Hamdy Elsafi

last: Mabrouk

state: NRW

address: pauwelsstraße 20

department: Helmholtz Institute of Biomedical Engineering

institute: RWTH-Aachen

data_processing:
Trimming of low-quality and sequancing primer: BBDuk v38
Psudo-alighnment, abudance estimation: Salmon v1.51
Genome_build: GRCh38
Supplementary_files_format_and_content: sample.sf is a salmon transcript abudance estimation file.

source_name: hiPSCs

growth_protocol: Seven iPSC-lines were generated from mesenchymal stromal cells (iPSC-102, iPSC-104, iPSC-106, and iPSC-3-11), blood (PT4-WT4, PT18-WT18), or human dermal fibroblasts (C2.3) by reprogramming with episomal plasmids or sendai virus, respectively. The study was approved by the local ethic committee and all samples were taken after written consent (EK206/09). The iPSC lines were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm2) in StemMACS iPS-Brew XF (Miltenyi Biotec). Pluripotency was validated by three lineage differentiation potential and Epi-Pluri-Score analysis, as described in our previous work (Lenz et al., 2015; doi.org/10.1038/srep08973). Micro-contact printing (µCP) was carried out to generate circular adhesion islands with different diameters that facilitate attachment of iPSCs. PDMS pillars were coated with vitronectin (10 µg/mL) for 45 minutes and then used as stamps on pretreated substrates. Stamps were brought into conformal contact with the substrate for at least 1 minute. Cells were seeded on the patterned substrates at 10,000 cells/cm2. Self-detaching EBs formed spontaneously from micro-contact printed substrates after 6-7 days in culture.

extract_protocol:
For Single-Cell RNA-Seq samples, colonies harvested at day 5, the cell culture medium was aspirated, 800 µL of Accutase were added on top of the cells, and they were incubated for 5 minutes at 37 °C After that, 1 mL of pre-warmed KO-DMEM were added to each sample and the cell were pipetted several time to create single cell suspension. Cells were then transferred to 15-mL falcon tubes. For processing of 3D aggregates, they were collected at day 8 from cell seeding into15 mL falcon tube and centrifuged at 100 g for 3 minutes. The supernatant was aspirated, and 1 mL of pre-warmed Accutase were added to each falcon tube for 9 mins at 37 °C. The aggregates were pipetted up and down several time to create single cell suspension. Falcons containing single cells were centrifuged again at 1000 RPM for 4 minutes. Then, they were re-suspended in 1 mL of PBS + 1 µL Y-27632 ROCK Inhibitor + 0.04% BSA. The suspension were filtered through 40 µm cell strainer to remove cell clumps. The cells were counted and centrifuged again, and the cells density was adjusted to 500-1000 cells/µL. Cells were kept on ice until further processing. For RNA-Seq experiment, self-detached aggregates or Spin-EBs were incubated in EB-Medium containing 10% FCS for 7 days. Samples were isolated at day 0, 3, and 7. Total RNA were isolated using Nucleospin RNA kit (Macherey-Nagel), Quality control was done with a NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, USA). RNA was stored at -80 until further processing.
For single-cell RNA-Seq, The cell suspension was processed by the chromium platform (V3) from 10X Genomics according to the manufacturer’s 3' protocol to obtain a sequencing library. The cells were deposited into the microfluidic platform provided by 10X Genomics. Chromium controller was used to partition cells into Gel Bead-In-EMulsions (GEMs). Cell lysis was carried out in the GEMs, which included a unique barcode for each bead. The Read1 was added during the GEMs lysis and cDNA construction. The barcoded cDNA was then purified using Dynabeads and amplified using PCR and random primers. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, i7 and i5 sample indexes, and Read 2 primers are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification. The library was then sequenced using Nextseq 550 to get paired-ended reads. For Bulk-RNA-seq experiment, the library preparation was carried out using QuantSeq 3´-mRNA (Lexgon) according to the manufacturer instruction. Sequencing was done using NovaSeq 6000 sequencer (Ilumina). Library preparation and sequencing was carried out by Life&Brain (Bonn, Germany).

tag: day

tag: eb-type

value: uCP-EB

value: Donor 2


title: Jlat 8.4 Hi-C (control)


title: human WBC, GB4030007 (iDNase-seq)


title: human WBC, GB4030009 (iDNase-seq)


title: Mettl3-RNAi HS m6A-IP SYS rep2

description:
m6A-IP-seq
Mettl3_RNAi.HS.sys.log2_m6A_input.bw
read_counts.txt.gz

value: SYS

value: 30 minute heat shock

value: Mettl3 RNAi


title: µCP-EB D7 - Donor 3

value: Donor 3


title: human WBC, GB4030005 (iDNase-seq)


title: Mettl3-RNAi HS input SYS rep1

description:
input for m6A-IP-seq
Mettl3_RNAi.HS.sys.log2_m6A_input.bw
read_counts.txt.gz


title: 41971

description: High-plane of nutrition


title: 42931

description: Moderate-plane of nutrition


title: 77860

description: Moderate-plane of nutrition


title: human WBC, GB4030006 (iDNase-seq)


title: µCP-EB D7 - Donor 1

value: Donor 1


title: 17855

description: High-plane of nutrition


title: human WBC, GB4030004 (iDNase-seq)


title: Mettl3-RNAi HS m6A-IP NEB rep3

description:
m6A-IP-seq
Mettl3_RNAi.HS.neb.log2_m6A_input.bw
read_counts.txt.gz

value: NEB


title: Jlat 10.6 Hi-C (control)

value: MboI in situ Hi-C


title: Mettl3-RNAi HS input SYS rep2


title: Mettl3-RNAi HS m6A-IP SYS rep1


title: Spin-EB D7 - Donor 3

value: Spin-EB


title: Mettl3-RNAi HS m6A-IP NEB rep2


title: human WBC, GB4030003 (iDNase-seq)

value: WBC


title: Mettl3-RNAi HS m6A-IP NEB rep1


title: Spin-EB D7 - Donor 2


title: human WBC, GB4030002 (iDNase-seq)


title: Spin-EB D7 - Donor 1


title: Mettl3-RNAi HS input NEB rep3

description:
input for m6A-IP-seq
Mettl3_RNAi.HS.neb.log2_m6A_input.bw
read_counts.txt.gz


title: 97854

description: Moderate-plane of nutrition

value: Moderate

value: Testes

value: Holstein-Friesian


title: Mettl3-RNAi HS input NEB rep2

value: head


title: human WBC, GB4030001 (iDNase-seq)


title: Mettl3-RNAi HS input NEB rep1


title: µCP-EB D3 - Donor 3


title: 21978

description: Moderate-plane of nutrition


title: 27823

description: High-plane of nutrition

value: High


title: PPHN lamb PAEC, 10PH

city: Cleveland

first: Devashis

last: Mukherjee

state: OH

address: 11100 Euclid Ave

department: Pediatrics

institute: Case Western Reserve University

description: small RNA library

data_processing:
Raw reads were processed by trim_galore (v0.2.5)
Trimmed reads were aligned to the sheep reference genome (oa3) using bowtie (v1.1.1)
miRNAs were detected with miRanalyzer (v0.3)
Assembly: oa3
Supplementary files format and content: Excel table reporting DE.miRs.output

source_name: main pulmonary artery

growth_protocol: Cells were grown in DMEM with FBS between passages 2-5 before RNA extraction

extract_protocol:
PAECs were isolated using 0.1% collagenase type A from the main pulmonary arteries and immunopurified using CD31 antibody-coated magnetic beads. Their identity was verified by staining for factor VIII antigen and acetylated low-density lipoprotein uptakeTotal RNA was extracted from cells using Trizol-chloroform extraction. RNA quantification was performed using Nanodrop (Thermofisher).
Illumina TruSeq small RNA library prep catalog number RS-200-0012.
small RNA seq

treatment_protocol: Fetal surgery was performed at ~125 days of gestation to ligate the ductus arteriosus in utero. This was kept ligated for 5-7 days, lambs were delivered at the end of this period and the lung was removed en bloc for tissue harvest.

value: main pulmonary artery

value: pulmonary artery endothelial cell

value: in utero ductal ligation for 5-7 days


title: 13745

description: High-plane of nutrition


title: PPHN lamb PAEC, 12PH

description: small RNA library


title: 47858

description: High-plane of nutrition


title: PPHN lamb PAEC, 11PH

description: small RNA library


title: Mettl3-RNAi basal m6A-IP SYS rep1

description:
m6A-IP-seq
Mettl3_RNAi.basal.sys.log2_m6A_input.bw
read_counts.txt.gz

value: basal


title: Mettl3-RNAi basal m6A-IP SYS rep2


title: µCP-EB D3 - Donor 2

value: uCP-EB

value: Donor 2


title: µCP-EB D3 - Donor 1


title: PPHN lamb PAEC, 9PH

description: small RNA library


title: Mettl3-RNAi basal input SYS rep2

description:
input for m6A-IP-seq
Mettl3_RNAi.basal.sys.log2_m6A_input.bw
read_counts.txt.gz

value: Mettl3 RNAi


title: 97821

description: Moderate-plane of nutrition


title: Spin-EB D3 - Donor 3

value: Donor 3


title: 93744

description: Moderate-plane of nutrition


title: Spin-EB D3 - Donor 2


title: 51980

description: Moderate-plane of nutrition


title: PPHN lamb PAEC, 8PH

description: small RNA library


title: Spin-EB D3 - Donor 1

value: Donor 1


title: Mettl3-RNAi basal input SYS rep1


title: PPHN lamb PAEC, 7PH

description: small RNA library


title: 47825

description: Moderate-plane of nutrition


title: 57826

description: High-plane of nutrition


title: Mettl3-RNAi basal m6A-IP NEB rep3

description:
m6A-IP-seq
Mettl3_RNAi.basal.neb.log2_m6A_input.bw
read_counts.txt.gz

value: NEB


title: Control lamb PAEC, 6CTR

description: small RNA library

value: sham surgery


title: µCP-EB D0 - Donor 3


title: µCP-EB D0 - Donor 2


title: 92928

description: Moderate-plane of nutrition


title: Control lamb PAEC, 3CTR

description: small RNA library


title: Spin-EB D0 - Donor 2

value: Spin-EB


title: Control lamb PAEC, 4CTR

description: small RNA library


title: Control lamb PAEC, 2CTR

description: small RNA library


title: 87886

description: Moderate-plane of nutrition

value: Moderate


title: Control lamb PAEC, 5CTR

description: small RNA library


title: 57867

description: High-plane of nutrition

value: Testes


title: µCP-EB D0 - Donor 1


title: Mettl3-RNAi basal input NEB rep2

description:
input for m6A-IP-seq
Mettl3_RNAi.basal.neb.log2_m6A_input.bw
read_counts.txt.gz


title: Mettl3-RNAi basal m6A-IP NEB rep1


title: 93760

description: High-plane of nutrition

value: Holstein-Friesian


title: 12937

description: High-plane of nutrition


title: Spin-EB D0 - Donor 3


title: Control lamb PAEC, 1CTR

description: small RNA library


title: Mettl3-RNAi basal input NEB rep1

value: head


title: Mettl3-RNAi basal input NEB rep3


title: Spin-EB D0 - Donor 1


title: Mettl3-RNAi basal m6A-IP NEB rep2


title: KO_Input_1

status: Public on Aug 25 2022

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Raw reads quality trimmed using trim-galore with default settings and assessed with fastqc
Surviving paired reads were then aligned against the mouse reference genome mm10 using bwa-mem
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
RPKM normalized bamCoverage files were produced using deeptools2
RPKM normalized bamCoverage files for two replicates of each condition were averaged and blacklisted regions were removed using deeptools2
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig files containing RPKM normalized ChIP-Seq signal for each sample and bigwig files of averaged replicates of each condition

source_name: Mouse Embronic Fibroblast

growth_protocol: WT and KO mouse embryonic fibroblasts (MEFs) were maintained and cultured with Dulbecco’s modified Eagle medium (DMEM) with high glucose, 10% fetal bovine serum (FBS) and 100 U/mL penicillin and 100 μg/mL streptomycin, in a humidified incubator with 5% CO2 at 37 °C.

extract_protocol:
Cells were crosslinked (two biological replicates per condition and input controls) using 1% formaldehyde (Sigma Cat. No. F8775) for 10 min followed by quenching with 0.125 M Glycine for 5 min and lysis with lysis buffer 1-LB1-(50 mM Hepes KOH pH 7.5, 10 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100). Nuclei were pelleted, collected and washed using lysis buffer 2-LB2- (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). This was followed by lysis using lysis buffer 3 LB3 (10 mM Tris-HCl pH 8; 100 mM NaCl, 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate, 0.5% N-laurylsarcosine). Chromatin was sheared using Qsonica Sonicator (4 cycles of 3 min at 70 % Amplitude), and then checked on 0.8% agarose gel. 100 μg of fragmented chromatin was mixed with ?. The protein-antibody immunocomplexes were recovered by the Pierce Protein A/G Magnetic Beads (Thermo-Scientific). Beads and attached immunocomplexes were washed twice using Low salt wash buffer (LS) (0.1% SDS; 2 mM EDTA, 1% Triton X-100, 20 mM Tris-HCl pH 8, 150 mM NaCl), and High Salt (HS) wash buffer (0.1% SDS, 2 mM EDTA, 1% Triton X-100, 20 mM Tris-HCl pH 8, 500 mM NaCl), respectively. The beads were resuspended in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS). De-crosslinking was achieved by adding 8 µL 5 M NaCl and incubating at 65 °C overnight. RNase A (1 µL 10 mg/mL) was added for a 30 min incubation at 37 °C. Then, 4 µL 0.5 M EDTA, 8 µL 1 M Tris-HCl, and 1 µL 20 mg/mL proteinase K (0.2 mg/mL) were added for a 2-hour incubation at 42 °C to digest the chromatin. DNA was purified by QIAquick PCR purification kit (Qiagen, Germantown, MD, USA) for qPCR analysis and sequencing.
ChIP-seq library preparation was done using the TruSeq Nano DNA Library Prep Kit (Illumina, San Diego, CA, USA) and then sequenced with the NextSeq550 sequencing platform (performed at the NYUAD Sequencing Center).

value: Mouse Embronic Fibroblast

tag: strain

value: BALB/c

tag: antibody

value: Input


title: KO_H3K27me3_2


title: KO_H3K27ac_2


title: KO_Input_2


title: KO_H3K27me3_1


title: KO_H3K4me_1


title: KO_H3K4me_2


title: KO_H3K9ac_1


title: KO_H3K9me3_1


title: KO_SNF2H_1


title: WT_H3K27me3_2

value: Wild Type


title: WT_H3K27me3_1


title: WT_H3K9me_1


title: WT_H3K9me_2


title: KO_H3K27ac_1


title: KO_SNF2H_2


title: WT_H3K27ac_2


title: WT_H3K9me3_2


title: WT_H3K9ac_2


title: WT_H3K9ac_1


title: KO_H3K9ac_2


title: WT_H3K27ac_1


title: WT_SNF2H_2


title: WT_Input_1


title: WT_Input_2


title: WT_H3K9me3_1


title: WT_SNF2H_1


title: KO_H3K9me3_2


title: zebrafish, RNA-seq, Eif4e1c +/+, rep 1 [pR1]

city: Columbus

first: Joseph

middle: Aaron

last: Goldman

state: Ohio

address: 119 Rightmire Hall, 1060 Carmack Road

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Fastq files were processed using FastQC (v0.11.8; RRID:SCR_014583) for quality control (QC) analysis. Pre-processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX-Toolkit (RRID:SCR_019035).  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers (UMIs). Cutadapt (RRID:SCR_011841) was used to trim 21-nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI.
The processed reads were aligned to GRCz11/danRer11 (assembly of the zebrafish genome; Genome Reference Consortium) using STAR v2.5.3a (RRID:SCR_004463). Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions (CDS) were obtained for each sample based on RiboProfiling function modules, TxDb.Drerio.UCSC.danRer11.refGene (v3.4.6; Annotation package for TxDb object(s); Team BC, 2019) and GenomicFeatures package (v1.46.1). Differential expression analysis was performed using the DESeq2 pipeline (version 1.26.0), based on the expressed raw reads.
Assembly: GRCz11/danRer11

organism: Danio rerio

source_name: heart

growth_protocol: Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching adulthood.

extract_protocol:
The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5-gauge needle syringe 20x on ice. Cell extracts (average OD 7) were treated with MNase (NEB), CaCl2 (5mM final concentration), and Turbo DNAse I (Invitrogen) at 25°C for 30 minutes. MNase digestion was stopped with SUPERase-inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns (Cytiva). Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS (Ambion). 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12,000 rpm (4°C). The aqueous phase was extracted and precipitated overnight at -20°C using glycoblue (ThermoFisher) and isopropanol followed by centrifugation for 30 minutes at 4C at 10,000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water.
Next-Flex smRNA seq kit v3

value: heart

value: Wt

value: Eif4e1c +/+


title: zebrafish, RNA-seq, Eif4e1c +/+, rep 2 [pR2]


title: zebrafish, Ribo-seq, Eif4e1c -/- rep2 [r_mR2]

data_processing:
Fastq files were processed using FastQC (v0.11.8; RRID:SCR_014583) for quality control (QC) analysis. Pre-processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX-Toolkit (RRID:SCR_019035).  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers (UMIs). Cutadapt (RRID:SCR_011841) was used to trim 21-nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI.
The processed reads were aligned to GRCz11/danRer11 (assembly of the zebrafish genome; Genome Reference Consortium) using STAR v2.5.3a (RRID:SCR_004463). Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions (CDS) were obtained for each sample based on RiboProfiling function modules, TxDb.Drerio.UCSC.danRer11.refGene (v3.4.6; Annotation package for TxDb object(s); Team BC, 2019) and GenomicFeatures package (v1.46.1). Differential expression analysis was performed using the DESeq2 pipeline (version 1.26.0), based on the expressed raw reads.
Assembly: GRCz11/danRer11
Library strategy: Ribo-seq

value: Mutant

value: Eif4e1c -/-


title: zebrafish, RNA-seq, Eif4e1c -/-, rep 1 [mR1]


title: zebrafish, Ribo-seq, Eif4e1c -/-, rep 1 [r_mR1]


title: Liver, Danlu Tongdu, 26 weeks, DLTD2

city: Beijing

first: Zhang

middle: Hai

last: Jing

address: A4, East Yinghua Street

department: Institute of chinese material medica

institute: China academy of chinese medical sciences

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>].
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample ...

organism: Rattus norvegicus

source_name: Liver

growth_protocol: The SPF Sprague Dawley rats used in this study were housed in polypropylene cages at an ambient temperature of 23°C (±3°C) and 40-70% relative humidity, with a 12:12 h light/dark cycle. Animals were provided with commercial food pellets and water ad libitum.

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA.Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: Rats in the control group (4 rats)  were treated with ultrapure water; rats in the high-dose group (4 rats)  were treated with 6.67 g/kg Danlu.

value: Sprague-Dawley

value: Liver

value: Danlu Tongdu


title: zebrafish, Ribo-seq, Eif4e1c +/+, rep 1 [r_pR1]


title: Liver, Danlu Tongdu, 26 weeks, DLTD3


title: zebrafish, RNA-seq, Eif4e1c -/-, rep 2 [mR2]


title: Liver, Danlu Tongdu, 26 weeks, DLTD1


title: Liver, ultrapure water, 26 weeks, Ctrl3

value: ultrapure water


title: zebrafish, Ribo-seq, Eif4e1c +/+, rep 2 [r_pR2]


title: Liver, ultrapure water, 26 weeks, Ctrl4


title: SCG_MBML2_TET

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.0). Mouse genome mm10 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: count matrix in csv

source_name: bone marrow

growth_protocol: 8wk-old C57Bl6/J mice (#000664) were ordered from the Jackson Laboratory, housed in our animal facility for at least 2 weeks and used for experiments between 10-12 weeks of age

extract_protocol:
To remove contaminating RBCs prior to sample isolation, all mice were first perfused with 10ml of 5mM EDTA/PBS at a flow rate of 5ml/min and then with 10ml PBS (without Ca/Mg) at a flow rate of 5ml/min. Samples were isolated from distinct microenvironments in the calvarium by a combination of plasma mediated laser ablation and micropipette aspiration (Image-seq samples, see manuscript for details)  or, for the control mice, by crushing the calvarial bone marrow.
Dissociation of tissues into single cells: All Image-seq and control samples were collected in Media 199 supplemented with 2% (v/v) FBS. Samples were pipetted up and down to generate a single cell suspension and a cell count performed. Samples were then transferred to the 10x genomics chip for cell encapsulation and lysis. Library preparation was performed using the 10x genomics single cell 3 gene expression V2 protocol.

treatment_protocol: Image-seq and Tet_AR mice were injected with calcium binding dye tetracyclin (TET) 2 days prior to the experiment and alizarin red (AR) on the day of the experiment. Wild-type (WT) control mice were vehicle injected (PBS).


title: SCG_MBML2_WT


title: SCG_MBML10_3WT


title: Liver, ultrapure water, 26 weeks, Ctrl2


title: SCG_MBML10_1TET_AR

tag: condition

value: WCBM


title: Liver, ultrapure water, 26 weeks, Ctrl1


title: SCG_MBML10_4TET_AR


title: SCG_MBML3_R

value: Image-seq


title: SCG_MBML9_D3


title: SCG_MBML5_M


title: SCG_MBML5_R


title: Liver, Danlu Tongdu, 26 weeks, DLTD4


title: SCG_MBML3_M


title: SCG_MBML8_D1


title: SCG_MBML8_D2


title: SCG_MBML7_R


title: SCG_MBML1_Low

description: MLL-AF9 mouse model of acute myeloid leukemia (AML) in which leukemia cells expresses GFP under the ubiquitin promoter at day 10 after transplantation.


title: SCG_MBML1_High


title: SCG_MBML7_M


title: SCG_MBML9_D1


title: Brain-Old-scRNAseq-rep2

city: Rochester

first: Xu

last: Zhang

state: MN

address: 200 First St SW

department: Physical Medicine and Rehabilitation

institute: Mayo Clinic

data_processing:
For scRNA-seq, raw data were processed with Cell Ranger (v3.0) (10X Genomics) and aligned to the mouse genome version mm10. Further analyses were carried out in R version 3.6.0 using the package Seurat version (v3.1.3)
Genome_build: mm10
Supplementary_files_format_and_content: tar file include barcodes.tsv, features.tsv, and matrix.mtx files from CellRanger

source_name: Brain

extract_protocol:
Mice were euthanized with a lethal dose of pentobarbital and were transcardially perfused with ice-cold PBS. Brains were immediately removed and processed for downstream applications. For single cell suspensions subjected to scRNA-seq, the hemibrain was separated from the cerebellum, rinsed with HBSS containing 1% glutamax, cut with a razor blade into approximately 10 pieces, and centrifuged in HBSS without calcium and magnesium containing 1% glutamax and 5% trehalose at 220 g (2 minutes, room temperature). The supernatant was aspirated, enzyme mix 1 from the Adult Brain Dissociation Kit (Miltenyi Biotec) was added at half concentration, and the tube was incubated for 15 minutes at 34 °C under slow continuous rotation. Enzyme mix 2 from the Adult Brain Dissociation Kit (Miltenyi Biotec) was added and the solution was dissociated by gentle titration with a 5 ml pipette, followed by 10 minutes at 34 °C under slow continuous rotation; this step was repeated one time. 10% ovumocoid protease inhibitor (Worthington) was added next, followed by 10 ml of wash buffer (HBSS with 0.5% BSA and 1% glutamax). This solution was filtered through a pre-wet 70um strainer with additional wash buffer added to flush cells through the filter. The filtered solution was passed through a pre-wet 40um strainer with additional wash buffer added to flush cells through and centrifuged at 220 g (8 minutes, room temperature). After aspirating the supernatant, the pellet was resuspended in 200ml wash buffer and centrifuged for 220 g (8 minutes, room temperature). After aspirating the supernatant, the pellet was resuspended in FACS buffer (HBSS with 0.5% BSA, 1% glutamax, and 5% trehalose) and centrifuged for 220 g (8 minutes, room temperature). The final pellet was resuspended in PBS on ice and immediately processed for scRNA-seq.
For scRNA-seq, the GEMs were collected for reverse transcription using Chromium Single Cell 3’ Reagent Kits (10X Genomics). Standard Illumina sequencing primers and a unique i7 Sample index were added to each cDNA for library construction.

tag: stain

tag: age

value: 24 month

value: brain

value: Mixed Cells


title: SCG_MBML10_2WT


title: Brain-Old-scRNAseq-rep4


title: Brain-Old-scRNAseq-rep3


title: SCG_MBML2_TET_AR


title: SCG_MBML5_D


title: Brain-Old-scRNAseq-rep1

value: 6 month


title: P8_mouse_lung_rep2

city: Lisboa

first: Francisca

middle: Ferreira

last: Vasconcelos

state: Lisboa

address: Av. Prof. Egas Moniz, Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular João Lobo Antunes

data_processing:
Raw reads generated per sample were uniquely mapped to the mm10 assembly and annotated to the Gencode vM14 transcriptome using TopHat2 (version 2.1.1) with Bowtie2 (version 2.3.4)
Gene expression levels were quantified with HTSeq-count (version 0.10.0)
Data preprocessing was done in R, with limma and edgeR packages, as follows: genes were removed when weakly expressed or associated to noninformative features ("no_feature","ambiguous", "too_low_aQual","not_aligned","alignment_not_unique"); and for features without at least 1 read per million in n of the samples, where n is the size of smallest group of replicates (3).
The counts per gene were normalized to counts per million (CPMs) by dividing it by the total number of mapped reads per sample and multiplying by 10^6.
Genome_build: mm10
For AS event-level analysis, raw reads were mapped to previously annotated AS events for the mouse reference assembly (mm10 vastdb.mm2.23.06.20) from VastDB (VastDB v2 released).
Abundance of AS events in Percent spliced in (PSI) values was estimated using VAST-TOOLS (version 2.5.1) align and combine commands
To calculate differential AS between each pair of time-points for the AS events, we used Vast-tools diff command. Vast-diff uses Bayesian inference followed by differential analysis to calculate dPSI (delta PSI) and minimum value difference (MV) between 2 samples for each AS event. We used a confidence interval of 95%, MV>10%
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample  (.txt)
Supplementary_files_format_and_content: Matrix table with CPMs for every gene and every sample (.txt)
Supplementary_files_format_and_content: Matrix table with PSIs for every alternative splicing event (VAST-tools) and every sample (.txt)

source_name: lung

extract_protocol:
Lungs were removed, flash frozen on liquid nitrogen. To extract and purify RNA, we used the RNeasy Plus Mini Kit (Qiagen), following manufacturers’ instructions.
RNA libraries were prepared for sequencing using standard Truseq RNA Library protocols.

value: lung


title: P8_mouse_lung_rep3


title: P8_mouse_lung_rep1


title: Brain-Young-scRNAseq-rep1


title: P5_mouse_lung_rep3


title: P5_mouse_lung_rep2


title: E18.5_mouse_lung_rep2


title: P5_mouse_lung_rep1


title: E18.5_mouse_lung_rep3


title: Brain-Young-scRNAseq-rep2


title: E18.5_mouse_lung_rep1


title: E15.5_mouse_lung_rep3


title: E15.5_mouse_lung_rep2


title: E15.5_mouse_lung_rep1


title: mouse_D7_10X

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Single-cell RNA seq, 10X Chromium

data_processing:
The 10X Genomics Cell Ranger pipeline v.2.1.1 was used to align raw sequencing reads to GRCm38 mouse genome and count the number of reads aligning to each gene. Quality control (QC), normalization and gene expression analysis was performed using the CRAN R package Seurat v.3.1.2 (Butler et al., 2018; Stuart et al., 2019) in R v.3.6.2. Cells with <5,000 UMI counts, <2,000 genes detected and >6% mitochondrial reads were excluded. Normalization was performed using SCTransform (Hafemeister and Satija, 2019) v.0.2.1 implemented in Seurat.
Genome_build: GRCm38
Supplementary_files_format_and_content: 10X Barcode file: Tsv files contain barcodes of detected cells.
10X feature file: Tsv files contain IDs of detected genes.
10X matrix file: Mtx files contain matrix of raw count values.
10X normalized count file: Txt files contain normalized and filtered count values with genes in rows and cells in columns.

source_name: Carotid artery

extract_protocol:
To generate the 10X D7 dataset, cells from ligated left common carotid arteries of five VSMC lineage-labeled animals (Myh11-EYFP-Ki67/RFP) 7 days after surgery were pooled. EYFP+ cells were isolated by FACS and enriched for proliferating RFP+EYFP+ cells: a total of 100 EYFP+RFP+ cells were supplemented with 20,000 unselected EYFP+ cells before loading onto a 10X Chromium system. Single cell preparation: Carotid arteries were dissected free of perivascular adipose tissue, cut open longitudinally and the endothelium was removed by gentle scraping with a cotton bud. Carotid arteries were then pre-digested in DMEM (Gibco) supplemented with 1 mg/mL Collagenase IV (Invitrogen) and 1 U/mL Elastase (Worthington) for 10 minutes at 37˚C to allow removal of the adventitial layer. The medial layer was transferred to fresh DMEM supplemented with 2.5 mg/mL Collagenase IV (Invitrogen) and 2.5 U/mL Elastase (Worthington) and digested to a single cell suspension at 37 ˚C.
A total of 20,000 cells were loaded onto a Chromium system (10x Genomics), amplified cDNA was generated using the 3’ Gene Expression v2 kit and sequenced using a paired end protocol (HiSeq 4000, Illumina).

tag: background


title: MEL202/i-shCtrl + doxycycline; biol rep 1

city: Leiden

first: Hailiang

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNAseq reads were aligned to human reference genome GRCh38 using GSNAP/GMAP version 2014-12-23.
Gene quantification was then performed using htseq-count version 0.6.1 with Gencode gene annotation obtained on 2015-03-24.
Assembly: GRCh38
Supplementary files format and content: TSV, gene raw count

growth_protocol: MEL202-derived cell lines were maintained in DMEM-F12/RPMI medium containing 10% tetracycline-verified FBS at 37 degrees, 5% CO2 in humidified atmosphere

extract_protocol:
miRNeasy kit (Qiagen, Hilden, Germany) and treated with DNAse (Qiagen) according to manufactures protocol
NEBNext Ultra Directional RNA Library Prep Kit for Illumina [NEB E7420S].

treatment_protocol: Expression of the shRNAs was induced by treatment with Doxycycline, 10 ng/ml, 48 hrs

tag: cell line

value: uveal melanoma

value: Ctrl knockdown

value: Doxycycline, 48 hrs


title: MEL202/i--shCtrl - doxycycline; biol rep 2

value: Vehicle, 48 hrs


title: MEL202/i-shCtrl + doxycycline; biol rep 3


title: MEL202/i--shCtrl - doxycycline; biol rep 3


title: MEL202/i-shCtrl + doxycycline; biol rep 2


title: MEL202/i-shMDMX #2 + doxycycline; biol rep 2

value: MDMX knockdown


title: MEL202/i-shMDMX #3 + doxycycline; biol rep 1


title: MEL202/i-shMDMX #1 + doxycycline; biol rep 3


title: MEL202/i-shMDMX #2 + doxycycline; biol rep 1


title: MEL202/i-shMDMX #1 + doxycycline; biol rep 2


title: MEL202/i-shMDMX #4 + doxycycline; biol rep 1


title: MEL202/i-shMDMX #3 + doxycycline; biol rep 3


title: MEL202/i-shMDMX #4 + doxycycline; biol rep 3


title: MEL202/i-shMDMX #3 + doxycycline; biol rep 2


title: MEL202/i-shMDMX #4 + doxycycline; biol rep 2


title: K2_3_1

city: Örebro

first: Robert

last: Kruse

address: Södra Grev Rosengatan 32

department: Kliniskt forskningslaboratorium

country: Sweden

institute: Örebro University

description: miRNA

data_processing:
The libraries were sequenced using NGS on HiSeq 2500 (Illumina) according to the manufacturer’s protocol, with single read sequencing of >10 million reads per sample. All pre-analytic processing and analyses of miRNA data were performed using the Strand NGS software suite version 3.3.1 (www.strand-ngs.com). All reads were subjected to adaptor trimming, followed by trimming of bases with a base quality ≤ 20. Trimmed reads were aligned and mapped to the human reference genome (Genome build: Homo sapiens, HG 19 (build 2009.06.14)) allowing up to one mismatch per uniquely aligned read. DESeq normalization of data was performed prior to statistical  and bioinformatic analyses
Assembly: Homo sapiens, HG 19 (build 2009.06.14)
Supplementary files format and content: DESeq normalized data

source_name: Placenta

extract_protocol:
Total RNA was extracted from 10–30 mg of each placental sample using the Allprep DNA/RNA/miRNA Universal Kit (50), catalogue no. 80224 (Qiagen, Nordic, Sollentuna, Sweden) according to the manufacturer´s instructions. RNA yield and purity were determined with a Nano-Drop ND-1000 Spectrophotometer (Nano-Drop Technology, Wilmington, DE, USA), and RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer´s instructions, as previously reported (10). All nineteen samples of RNA were of high quality with an optical density 260/280 ratio of 1.8–2.2 and an RNA integrity number ≥ 8.
Small RNA libraries were generated with Illumina’s Small RNA sample preparation protocol (TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA)) according to the manufacturer’s instructions

value: Placenta

tag: fetal sex

value: M

value: Healthy


title: K4_3_1

description: miRNA

value: F


title: K3_3_2

description: miRNA


title: K16_3_1

description: miRNA


title: K2_3_2

description: miRNA


title: K7_3_1

description: miRNA


title: K9_3_2

description: miRNA


title: K3_3_1

description: miRNA


title: K16_3_2

description: miRNA


title: K8_3_1

description: miRNA


title: K14_3_2

description: miRNA


title: K7_3_2

description: miRNA


title: MEL202/i-shCtrl - doxycycline; biol rep 1


title: K1_3_1

description: miRNA


title: K15_3_1

description: miRNA


title: MEL202/i-shMDMX #1 + doxycycline; biol rep 1


title: K14_3_1

description: miRNA


title: K10_3_2

description: miRNA


title: K4_3_2

description: miRNA


title: WM266-4 cells, Suspension, 25mM Glucose, replicate #1

city: Logroño

first: Ignacio

last: Larrayoz

address: C\ Piqueras 98, Ed CIBIR

department: Oncology Area

country: Spain

institute: CIBIR

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore 0.6, using default parameters
Read quality was checked for each sample using FastQC v0.11
Trimmed sequence reads were mapped to GRCh38 using STAR aligner v2.7.4
Read count extraction and normalization were performed using FeatureCounts from Subread (v1.6.2) R package and DESeq2 (v1.32) R package
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include DESeq2-normalized values for each Sample

growth_protocol: 501mel WM2666-4 melanoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina´s TruSeq RNA Library Prep Kit v2 following manufacturer's protocols.

treatment_protocol: Medium contained either 25 mM or 5 mM glucose. Cells were grown in adherent or suspension conditions

value: Melanoma, undifferentiated, invasive

value: Grown in suspension, 25 mM Glucose


title: K12_3_2

description: miRNA


title: WM266-4 cells, Suspension, 5mM Glucose, replicate #1

value: Grown in suspension, 5 mM Glucose


title: WM266-4 cells, Adherent, 5mM Glucose, replicate #3

value: Adherent conditions, 5 mM Glucose


title: WM266-4 cells, Suspension, 25mM Glucose, replicate #3


title: WM266-4 cells, Suspension, 5mM Glucose, replicate #3


title: WM266-4 cells, Adherent, 5mM Glucose, replicate #1


title: K10_3_1

description: miRNA


title: WM266-4 cells, Suspension, 25mM Glucose, replicate #2


title: WM266-4 cells, Adherent, 25mM Glucose, replicate #3

value: Adherent conditions, 25 mM Glucose


title: WM266-4 cells, Adherent, 5mM Glucose, replicate #2


title: 501mel cells, Suspension, 25mM Glucose, replicate #3

value: Melanoma, differentiated, proliferative


title: 501mel cells, Suspension, 25mM Glucose, replicate #1


title: 501mel cells, Adherent, 5mM Glucose, replicate #3


title: 501mel cells, Suspension, 5mM Glucose, replicate #2


title: WM266-4 cells, Adherent, 25mM Glucose, replicate #2


title: 501mel cells, Suspension, 25mM Glucose, replicate #2


title: 501mel cells, Adherent, 25mM Glucose, replicate #3


title: 501mel cells, Suspension, 5mM Glucose, replicate #1


title: 501mel cells, Adherent, 25mM Glucose, replicate #1


title: 501mel cells, Adherent, 25mM Glucose, replicate #2


title: 501mel cells, Adherent, 5mM Glucose, replicate #2


title: 501mel cells, Adherent, 5mM Glucose, replicate #1


title: WM266-4 cells, Suspension, 5mM Glucose, replicate #2


title: 501mel cells, Suspension, 5mM Glucose, replicate #3


title: WM266-4 cells, Adherent, 25mM Glucose, replicate #1


title: 697_0hr_H3K27ac_HiChIP

city: Memphis

first: Daniel

last: Savic

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
Library strategy: Hi-ChIP
Reads were mapped to the human genome using bwa mem
Alignments were converted into .pairs files
Pairs files were used as input for HiChIP Loop Calling using FitHiChIP
All default parameters provided by the Dovetail Genomics HiChIP data processing documentation were followed, aside from mapping to hg19 instead of hg38
Genome_build: hg19
Supplementary_files_format_and_content: *PREFIX*.interactions_FitHiC.bed: Lists all input interactions along with their significance (p-value and FDR) computed using FitHiChIP and *PREFIX*.interactions_FitHiC_Q”qval”.bed: FitHiChIP generated set of significant interactions according to the q-value threshold (QVALUE) specified in parameter

source_name: 697 (ALL cell line)

growth_protocol: Nalm6 and 697 cells were maintained with RPMI-1640 with 10% charcoal-stripped FBS, 2mM Glutamine, and Pen/Strep

extract_protocol:
Extraction and sample prep was conducted following the recommended guidelines from Dovetail Genomics Sample Preparation Guidelines.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with prednisolone at a concentration of 5uM (Nalm6 cells) or 10uM (697 cells) for 6 or 24 hours

value: ALL

tag: replicate


title: 697_6hr_H3K27ac_HiChIP

value: PRED (10uM, 6hrs)


title: 697_24hr_H3K27ac_HiChIP

value: PRED (10uM, 24hrs)


title: Nalm6_6hr_H3K27ac_HiChIP

source_name: Nalm6 (ALL cell line)

value: PRED (5uM, 6hrs)


title: Nalm6_0hr_H3K27ac_HiChIP


title: WT, 60 min high light (800µE), replicate 3

type: RNA

city: ACTON

first: Marten

last: Moore

state: ACT

address: 134 Linnaeus Way

department: Research School of Biology

institute: The Australian National University

description:
gene expression from WT at 60 HL
WT_HL_REP_3

hyb_protocol: 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Arabidopsis Gene 1.0 ST arrays for 16 h at 45 °C in a rotating chamber

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de). Summarized probe set signals were calculated by using the RMA (1) algorithm with the Affymetrix GeneChip Expression Console Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.

label: biotin

source_name: WT, 60 min high light (800µE)

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 15 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: Arabidopsis seeds were sown onto moist soil (Seed Raising and Cutting Mix, Martins, NSW, Australia) supplemented with 1 g/L dry volume of soil Osmocote Exact Mini slow release fertilizer (Scotts, NSW, Australia) and 1 L of 0.3 % (v/v) AzaMax (OCP, NSW, Australia). Seeds were covered with a plastic hood and stratified at 4 °C in the dark for at least 72 hours to break dormancy and coordinate germination. Stratified seeds were transferred to a temperature controlled Conviron S10H growth chamber (Conviron, Winnipeg, MB, Canada), fitted with a mixture of 250 W metal halide lamps (Venture Lighting, MH 250W/U) and high pressure sodium lamps (Phillips, SON‐T 250 W E E40 SL/12), for cultivation under a 10-hour photoperiod (08:00-18:00) of 80-100 μ mol photons m-2 s -1, 22.5/20.5 °C day/night temperatures, and 57/55 % day/night relative humidity.

extract_protocol: mRNA was extracted following the QIAGEN RNA extraction kit.

treatment_protocol: Three weeks old plants were transfered to 8 µmol photons m-2 s-1 (LL) for 10 days. Plants were transferred to 800 µmol photons m-2 s-1 (HL) for 10 min, while control plants remained in LL. Whole rosettes were harvested under control and HL conditions in the midday point of the light period to exclude circadian effects and immediately frozen in liquid nitrogen and stored at -80°C.

value: whole rosettes

tag: number of plants

tag: biological replicate number

value: WT (Col-0)

value: high light (800µE) HL


title: sap3 KO, low light control (8µE), replicate 1

description:
gene expression from sap3 KO at LL control
SAP3_LL_REP_1

source_name: sap3 KO, low light control (8µE)

tag: tissue

value: SAP3 KO

value: low light (8µE) LL


title: Brain CCR2-DTR Trichinella-Infected Rep 1

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software (Version 11.0.1) platform for analysis.
Imported reads were trimmed to remove adapters and low quality reads using CLC Genomics Workbench.
The reads are mapped to reference genome Mus musculus genome GRCm38.
The aligned reads were obtained using the RNA-Seq Analysis Tool of CLC Genomics Workbench using default settings.
Comparison of samples was performed using the "Differential Expression in RNA seq" function in CLC Genomics Workbench.
Genome_build: GRCm38
Supplementary_files_format_and_content: Total_counts_merged.csv: Comma-delimited file for CLC hit counts.

extract_protocol:
Brain total cellular RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Thermo Fisher Scientific). The quality of RNA was first checked for integrity on an Agilent Bioanalyzer 2100; samples with RNA integrity number (RIN) >7.0 were used for subsequent processing. Total RNA was subjected to two rounds of poly(A) selection using oligo-d(T)25 magnetic beads (New England Biolabs). Illumina compatible RNAseq library was prepared using NEB next ultra RNAseq library preparation kit. The cDNA libraries were purified using AmpureXP beads and quantified on an Agilent Bioanalyzer and qubit analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Brain

value: 8-12 weeks (adult)

tag: treatment

value: Trichinella spiralis infection


title: WT, 60 min high light (800µE), replicate 2

description:
gene expression from WT at 60 HL
WT_HL_REP_2


title: sap3 KO, 60 min high light (800µE), replicate 3

description:
gene expression from sap3 KO at 60 HL
SAP3_HL_REP_3

source_name: sap3 KO, 60 min high light (800µE)


title: Brain CCR2-DTR Trichinella-Infected Rep 2


title: sap3 KO, low light control (8µE), replicate 3

description:
gene expression from sap3 KO at LL control
SAP3_LL_REP_3


title: WT, low light control (8µE), replicate 1

description:
gene expression from WT at LL control
WT_LL_REP_1

source_name: WT, low light control (8µE)


title: Brain CCR2-DTR Naïve Rep2

value: Naive


title: Nalm6_24hr_H3K27ac_HiChIP

tag: cell type

value: PRED (5uM, 24hrs)


title: WT, 60 min high light (800µE), replicate 1

description:
gene expression from WT at 60 HL
WT_HL_REP_1

tag: genotype


title: Brain CCR2-DTR Naïve Rep1


title: Brain CCR2-DTR Trichinella-Infected Rep 3


title: WT, low light control (8µE), replicate 3

description:
gene expression from WT at LL control
WT_LL_REP_3


title: Brain WT Trichinella-Infected Rep3

value: WT


title: Brain WT Trichinella-Infected Rep2


title: Brain CCR2-DTR Naïve Rep3


title: sap3 KO, 60 min high light (800µE), replicate 2

description:
gene expression from sap3 KO at 60 HL
SAP3_HL_REP_2


title: Brain WT Trichinella-Infected Rep1


title: Brain WT Naive Rep2


title: Brain WT Naive Rep3


title: WT, low light control (8µE), replicate 2

description:
gene expression from WT at LL control
WT_LL_REP_2