title: Progeny 8 of cross 2121, high-bruising group, biol rep 2

value: mechanical impact (bruising)


title: 081021_PY01_Somatic

status: Public on Nov 29 2022

type: SRA

city: Dunedin

first: Donna

last: Bond

address: 270 Great King Street

department: Department of Anatomy

country: New Zealand

institute: University of Otago

library_source: genomic

data_processing:
Raw reads were trimmed using Trim Galore! (v0.4.2) by removing 10 bp from the 5’ end of all reads and removing low-quality base calls (Phred score < 20). Bismark (v0.19.0), with the -pbat option, was used to map the trimmed reads to the possum genome reference (GCA_011100635). The Bismark output report was used to determine the global methylation in the CG dinucleotide context (calculated as the proportion of total methylated cytosines over total cytosines). The bisulfite non-conversion rate was estimated by calculating the proportion of non-CG methylation.
Assembly: Trichosurus vulpecula (GCA_011100635.1)
Supplementary files format and content: tab-delimited text file that includes Bismark mapping report for each sample

molecule: genomic DNA

organism: Trichosurus vulpecula

source_name: Somatic

extract_protocol:
Gonads were collected from male pouch young aged between 7 and 106 days postpartum (n=17). Germ cells were isolated from gonads using the isolation protocol outlined in Suzuki et al (2013; PMID: 23732002). The resulting pellet was resuspended in Zombie Near-Infra Red Viability Dye (BioLegend) and incubated at room temperature for 20 min. The lysate was washed in 5 % FBS (in PBS), then resuspended in SSEA1 monoclonal antibody (Invitrogen, MC-480) conjugated to DyLight 488 (1:300 in PBS/5% FBS; Invitrogen, MA1-022-D488) on ice for 30 min. The lysate was then washed, resuspended in sort buffer (5% FBS, 0.5 mM EDTA in PBS) and kept on ice prior to cell sorting. Germ cells were isolated from the cell lysate using a BD FACSAria Fusion which detects GFP using a 488 argon laser (BD Biosciences). A gonadal cell profile was produced using forward scatter (FSC) and side scatter (SSC) and was gated to exclude doublets and dead cells. GFP-negative cells (somatic cells) were sorted as negative controls into 0.2 % Triton-X and stored at -80 °C.
Bisulfite conversion and library preparation from low cell input followed the single cell bisulfite sequencing protocol by Clark et al., 2017 (PMID: 28182018)

tag: Sex

value: Male

tag: cell type

value: Somatic

tag: developmental stage

value: 27 days postpartum

tag: treatment

value: GFP (SSEA1) negative

tag: number of_cells


title: Progeny 6 of cross 2121, high-bruising group, biol rep 2

city: Lincoln

first: Susan

last: Thomson

address: 74 Gerald Street

department: New Cultivar Innovation

institute: The New Zealand Institute for Plant & Food Research LTD

library_source: transcriptomic single cell

data_processing:
Read quality assessed with FastQC v0.11.7
rRNA contaminants removed with SortMeRNA with default parameters
Trimming performed with Bbtools v37.93 BBDuk (forcetrimleft = 15, trimpolyg = 30, k = 13, qtrim = r, trimq = 10, minlength = 50)
Alignment to reference genome and counting number of reads aligned to each gene using STAR v2.6.1 (alignMatesGapMax = 20000, outQSconversionAdd = -31, outFilterScoreMinOverLread = 0, outFilterMatchNminOverLread = 0, outFilterMatchNmin = 40, alignSJDBoverhangMin = 10, alignIntronMax = 200000, quantMode = ‘GeneCounts’)
Genes with at least 5 samples with less than 5 reads were filtered out (using the R software)
Assembly: PGSC-DM (genome assembly version v4.03 and gene annotation v4.03)
Supplementary files format and content: Comma-delimited (csv) file contains raw read counts for each sample (rows = genes, columns = samples). First column corresponds to the gene ID

molecule: polyA RNA

organism: Solanum tuberosum

source_name: tuber

extract_protocol:
RNA was extracted using the PureLink Plant RNA Reagent following manufacturer’s protocols, then incubating at -20degrees Celsuis for 3 hours in a lithium chloride solution
RNA libraries for ssRNA-Seq were prepared using a Lexogen SENSE mRNA polyA library, according to manufacturer’s protocols.

treatment_protocol: Tubers were bruised by letting a lead weight fall from controlled height on the tuber (zone of impact recorded by inking the weight before bruising)

tag: tissue

value: tuber

tag: genotype

tag: time

value: 2h post-bruising


title: Input ChIPseq sample 4, activated CD4 cells

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

description: mapped to HG38

data_processing:
bcl conversion and demultiplexing (bcl2fastq), to fastq files
fastq mapping to hg38 reference (STAR, default parameters apart alignIntronMax flag set to 1 for end-to-end mapping)
quality control (MultiQC v.0.9dev0, default parameters)
peak calling (MACS2, narrow peaks, default parameters)
peak filtering and merging (MACS2, peaks with enrichment versus surrounding region and input (adjusted p<10-5) selected, >=1bp overlapping peaks in four samples merged to single annotation and further used as “survivin-ChIP peaks” (“cmd=annotatePeaks.pl peaks/peaksMrg.txt hg38 -pc 1 -noadj -d”  for all four samples))
Genome_build: HG38
Supplementary_files_format_and_content: matrix with peak location (chromosome, strand, start, stop), peak score and sample redundancy in S1-S4

organism: Homo sapiens

source_name: Primary activated CD4 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells, culture activated with ConA+LPS for 72h

extract_protocol:
EpiTect ChIP OneDay kit (Qiagen), quality control TapeStation (Agilent, Santa Clara, CA, USA)
ThruPLEX (Rubicon)
Hiseq2000,Illumina, single end, default parameters (100bp reads)

treatment_protocol: ChIP with anti-Survivin (2 microg/ml, 10811, SantaCruz Biotechnology)

tag: agent

value: ConA+LPS

tag: antibody

value: Input


title: 250822_PY02_PGC

source_name: PGC

extract_protocol:
Gonads were collected from male pouch young aged between 7 and 106 days postpartum (n=17). Germ cells were isolated from gonads using the isolation protocol outlined in Suzuki et al (2013; PMID: 23732002). The resulting pellet was resuspended in Zombie Near-Infra Red Viability Dye (BioLegend) and incubated at room temperature for 20 min. The lysate was washed in 5 % FBS (in PBS), then resuspended in SSEA1 monoclonal antibody (Invitrogen, MC-480) conjugated to DyLight 488 (1:300 in PBS/5% FBS; Invitrogen, MA1-022-D488) on ice for 30 min. The lysate was then washed, resuspended in sort buffer (5% FBS, 0.5 mM EDTA in PBS) and kept on ice prior to cell sorting. Germ cells were isolated from the cell lysate using a BD FACSAria Fusion which detects GFP using a 488 argon laser (BD Biosciences). A gonadal cell profile was produced using forward scatter (FSC) and side scatter (SSC) and was gated to exclude doublets and dead cells. Germ cells were identified as a small subpopulation that were very bright (GFP >10^4) with higher SSC (approx. 0.1 % of total cells). This population was gated conservatively, sorted into 0.2 % Triton-X and stored at -80 °C.
Bisulfite conversion and library preparation from low cell input followed the single cell bisulfite sequencing protocol by Clark et al., 2017 (PMID: 28182018)

value: PGC

value: 26 days postpartum

value: GFP (SSEA1) sorted


title: Input ChIPseq sample 2, activated CD4 cells

description: mapped to HG38


title: Healthy #7 (H7)

city: Aurora

first: Christophe

last: Langouët-Astrié

state: CO

department: Pulmonary Sciences and Critical Care

country: USA

institute: University of Colorado Denver, Anschutz

description: Gene expression data from total lungs treated with IN saline on D0 and IT Saline on D10

library_source: transcriptomic

data_processing:
Illumina reads were trimmed for adaptor sequence and for quality in CLC Genomics Workbench (v.21.0.5)
Trimmed sequences were mapped to to the reference genome sequence of Mus musculus assembly mm10, with the parameters: mismatch cost, 2; insertion and deletion cost, 3; length and similarity fraction, 0.8.
Uniquely mapped transcripts from each sample were exported from CLC Genomics Workbench and used for normalization and differential gene expression analysis with an R package, DESeq2 version 1.32.0
Assembly: mm10
Supplementary files format and content: MRSA_gene_exp_diff contains differential gene expression between MRSA vs Control treatment. PR8_gene_exp_diff contains differential gene expression between PR8 vs Control treatment. PR8MRSA_gene_exp_diff contains differential gene expression between PR8+MRSA vs Control treatment. All files includes mouse gene names, baseMean, log2FoldChange, IfcSE, stat, pvalue, padj. Raw_gene_counts_matrix contains uniquely mapped transcripts for each sample with gene name and ENSEMBL ID.

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: USA300 was cultured in TSB from frozen stock for 18-24 hours. Overnight culture was diluted 1:50 and was incubated for 2.5 hours. Samples were centrifuged for 15 min at 4°C, then the pellet was resuspended in PBS,  centrifuged for 3 min at room temperature, and resuspended in saline. The opitical density of the bacterial suspension was measured and diluted three times to ensure bacterial samples were at desired optical density and bacterial concentration (1*10^8 CFU/30uL). Serial dilutions of the bacterial suspension was plated on TSB plates in triplicate and incubated for 24 hours at 37°C to confirm bacterial concentration.

extract_protocol:
Lungs were removed, snap frozen, homogenized, and RNA isolated using Qiagen RNeasy Midi Kit (Cat#75144).
RNA libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit (Cat#R3000) with 1 ug of total RNA for the construction of sequencing libraries. Invitrogen ERCC spike in controls (Cat#4456740) were added to all samples

treatment_protocol: Mice were intranasally (IN) administered with saline or PR8 (30k FFU). 10 days (D10) post-IN administration, mice were intratracheally (IT) administered saline or MRSA (1*10^8 CFU/30uL) and were left to recover for 24 hours.

value: Lung

tag: strain

tag: gender


title: Progeny 7 of cross 2121, not used in DE analysis, biol rep 1


title: 140421_PY02_Somatic

value: 16 days postpartum


title: Survivin ChIPseq sample 1, activated CD4 cells

description: mapped to HG38

value: Survivin


title: Input ChIPseq sample 3, activated CD4 cells

description: mapped to HG38


title: 250822_PY02_Somatic


title: mammary glands, T=18 weeks post injection

city: Amsterdam

first: Roebi

middle: de

last: Bruijn

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
filtered_feature_bc_matrix_5920_houthuijzen.h5
adata_5920_houthuijzen.h5

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: filtered output of cellranger h5 format to load into single cell analysis programs
Supplementary files format and content: h5 format object of scanpy with annotations used for the paper

source_name: mammary gland

extract_protocol:
Cre-injected glands were harvested 6, 12 or 18 weeks after injected. PBS-injected glands were harvested 12 weeks after injection. Glands/tumors were processed into a single cell suspension as described in the section ‘flow cytometry analysis’. Samples were stained using the following antibodies: CD31- APC, CD45-AF700, EpCAM-FITC and CD49f-PE-Cy7. Fibroblasts were considered negative for all mentioned markers. Sorted fibroblasts were spun down and frozen in FCS + 10% DMSO until use. On day of scRNA sequencing, samples were thawed, checked for viability by flow cytometry (percentage of dapi-negative cells was above 75% for all samples). Cells were resuspended 1000 cells/ul in 1xPBS containing 0.04% weight/volume BSA (400 ug/ml) and for each sample the Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding.
Per sample each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries were prepared according to the manufacturer’s protocol “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1” (CG000204, 10X Genomics). All four Single Cell 3’ Gene Expression libraries were quantified on a 2100 Bioanalyzer Instrument following the manufacturer’s protocol “Agilent DNA 7500 kit” (G2938-90024, Agilent Technologies). These Single Cell 3’ Gene Expression libraries were combined to create one sequence library pool which was quantified by qPCR, according to manufacturer’s protocol “KAPA Library Quantification Kit Illumina® Platforms” (KR0405, KAPA Biosystems). The NextSeq 550 Illumina sequencing system was used for paired end sequencing of the Single Cell 3’ Gene Expression libraries at a sequencing depth of approximately 18.000 reads pairs/cell. NextSeq 550 paired end sequencing was performed using 28 cycles for Read 1, 8 cycles for Read i7 and 56 cycles for Read 2, using NextSeq 500/550 High Output Kit v2.5 (75 Cycles) Reagent Kit (PN 20024906, Illumina).

value: mammary gland

tag: cell line

value: fibroblasts

value: intraductal injection lenti-cre (T=18 weeks)


title: 081021_PY01_PGC

value: Male


title: 090421_PY02_Somatic

value: Somatic

value: 13 days postpartum


title: Progeny 4 of cross 2121, high-bruising group, biol rep 1

value: mechanical impact (bruising)


title: Person C_CD4_IFNg_YM155, 24h

data_processing:
Aligned: STAR,  Ref.genome: Homo_sapiens.GRCh38.dna.primary_assembly.fa (Ensembl),
quantification: featureCounts
Genome_build: HG38
Supplementary_files_format_and_content: matrix with ENS number and samples in each one column

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells, culture activated with anti-CD3, 24h total

extract_protocol: Total RNA purification (Norgen, Ontario, Canada)

treatment_protocol: Treated with survivin inhibitor YM155 (0 or 10 ng/ml), IFNg last 2 h

value: IFNg

tag: time point

value: 10 ng/ml YM155

tag: person

value: C


title: Survivin ChIPseq sample 3, activated CD4 cells

description: mapped to HG38

value: ConA+LPS


title: Input ChIPseq sample 1, activated CD4 cells

description: mapped to HG38

value: Input


title: 110822_PY01_Somatic

value: 12 days postpartum

value: GFP (SSEA1) negative


title: Progeny 5 of cross 2121, not used in DE analysis, biol rep 1

value: tuber

value: 2h post-bruising


title: Progeny 3 of cross 2121, low-bruising group, biol rep 2


title: mammary glands, T=0 control

value: intraductal injection PBS (T=12 weeks)


title: mammary glands, T=6 weeks post injection

value: mammary gland

value: intraductal injection lenti-cre (T=6 weeks)


title: Survivin ChIPseq sample 2, activated CD4 cells

description: mapped to HG38

value: Survivin


title: Progeny 2 of cross 2121, not used in DE analysis, biol rep 2


title: 040822_PY01_Somatic

value: Male

value: 34 days postpartum


title: 140421_PY02_PGC

value: PGC

value: 16 days postpartum

value: GFP (SSEA1) sorted


title: rrb-1::degron; eft-3p::tir-1, 1 mM auxin, replicate 3

city: Austin

first: Elif

last: Sarinay Cenik

state: TX

address: NHB 2.606, Stop A5000 100 East 24th St.

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Reads were trimmed using fastp with the Nextera adapter sequence specified.
Trimmed reads were aligned using bowtie 2 with parameters ` --very-sensitive -X 2000`.
Duplicate reads were marked with SAMBLASTER.
SAM files were sorted, indexed, and compressed using SAMtools.
BAM files were filtered using Sambamba view with parameters `--filter "mapping_quality >= 10 and not ref_name == 'MtDNA' and not unmapped" --format bam --with-header` then sorted and indexed using Sambamba.
Filtered BAM files were converted to BED files with bedTools bamtobed.
Peaks were called on BED files using MACS2 with parameters `--format BED --gsize ce --keep-dup 1 --nolambda --nomodel --extsize 150 --shift 75`.
All narrowPeaks files were merged using Homer mergePeaks with options `-d given -gsize ce`.
featureCounts was used to count reads within merged peaks with the option `--ignoreDup` set to prevent counting duplicate reads.
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text files containing a header line, peak information, and raw count of reads within peaks

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: C. elegans strains were maintained and grown at 16°C or 20°C on peptone enriched NGM agar plates seeded with a lawn of E. coli OP50 bacteria. To obtain synchronized embryos, a standard bleaching procedure was used.

extract_protocol: Synchronized larvae were collected in 50 mM NaCl. Bacteria were cleaned from worms by sedimentation through 5 % sucrose in 50 mM NaCl at 400g for 1 minute with subsequent washes in 50 mM NaCl. At least 40,000 larvae were collected for each condition. Batches of larvae were evenly split into four replicates and buffer was exchanged to Nuclei Wash Buffer (NWB): 10 mMTris-HCl pH 7.5, 40 mM NaCl, 90 mM KCl, 3 mM MgCl2, 0.2 mM DTT, 0.5 mM Spermidine, 0.25 mM Spermine, and 1 X Protease Inhibitor Cocktail. Larvae pelleted in NWB were snap frozen in liquid nitrogen and stored at -70°C.  In order to minimize the potential confounding effects of batch on the experimental design, one replicate of each of the strains were processed concurrently for four total batches of four replicates. To isolate nuclei from larvae, worm pellets were thawed on ice. Buffer was transferred for thawed larvae to Nuclei Prep Buffer (NPB): 10 mMTris-HCl pH 7.5, 40 mM NaCl, 90 mM KCl, 3 mM MgCl2, 0.2 mM DTT, 0.5 mM Spermidine, 0.25 mM Spermine, 0.1 % Triton X-100, 0.1 % IGEPAL CA-630, and 1 X Protease Inhibitor Cocktail. Worms were transferred to a 2 mL dounce homogenizer that was pre-chilled in the refrigerator and kept on ice. Worms were initially broken by 15 strokes with homogenizer pestle A, a short rest on ice, and 15 more strokes with pestle A. Nuclei were released from broken worms by 25 strokes with pestle B, a short rest on ice, and 25 more strokes with pestle B. Debris was pelleted by a low speed spin of the homogenate for 5 minutes at 100g at 4°C. To pellet nuclei, the supernatant was taken from the low speed spin and sedimented for 10 minutes at 2000g at 4°C. Meanwhile, more nuclei were released by a second round of 25 strokes with pestle B, a short rest on ice, and 25 more strokes with pestle B. Debris was pelleted as above, and nuclei were pelleted as above in the same tube as the previous nuclei pellet. Nuclei yields were further increased with light sonication. Debris was resuspended in 300 μL total NPB and was sonicated in a Diagenode Bioruptor on Low power for 2 cycles of 30 seconds ON / 30 seconds OFF. Volume was brought to 1 mL total, and debris was removed and nuclei pelleted in the same tube as above. Nuclei were subjected to a buffer exchange and cleanup step to further remove any debris. The nuclei pellet was resuspended in 1 mL Tagmentation Reaction Buffer (TRB): 1 X Tagment DNA buffer (10 % Dimethylformamide, 10 mM Tris-HCl pH 7.5, 10 mM MgCl2), 0.33 X PBS, 0.01 % Digitonin, 0.1 % Tween-20. Debris was pelleted as above, and the supernatant was moved to a new tube and nuclei were pelleted as above. Nuclei were cleaned a final time by resuspending in TRB and pelleting. The supernatant was carefully removed to leave about 50 – 60 μL of supernatant without disturbing the nuclei pellet.  Nuclei were stained with DAPI and counted using a hemocytometer. Nuclei were tagmented by taking an aliquot of 50,000 nuclei, bringing the total reaction volume to 47.5 μL with TRB, and adding 2.5 μL TDE1 tagmentase. The tagmentation reaction was incubated for 30 minutes at 37°C with shaking. Immediately after the reaction concluded, reactions were cleaned up using the Zymo DNA Clean & Concentrator-5 kit.  Cleaned up tagmented DNA was added to a PCR reaction mix with 1.25 µM each Nextera i5 and i7 adapters and NEBNext High-fidelity 2X PCR Master Mix. Libraries were amplified with an initial extension and denaturation step of 5 minutes at 72°C and 30 seconds at 98°C followed by 12 cycles of 10 seconds at 98°C, 30 seconds at 63°C, and 1 minute at 72°C, with a final extension of 10 minutes at 72°C. Adapter contamination was initially removed with the Zymo DNA Clean & Concentrator-5 kit, and library size distributions were checked by running on a gel. Libraries were subjected to a final cleanup with 1.8 X AMPure XP beads.

treatment_protocol: Bleach synchronized embryos were placed on NGM agar plates with a lawn of OP50 bacteria and supplemented with 1 mM auxin. Larvae were synchronized at the L1 stage by allowing the embryos to hatch and develop at 23°C for 18 hours for strains with no tir-1 and 24 hours for strains with tir-1 as these have a growth delay.

value: Whole animal

value: rrb-1::degron; eft-3p::tir-1

value: 1 mM auxin


title: rrb-1::degron; eft-3p::tir-1, 1 mM auxin, replicate 4


title: mammary glands, T=12 weeks post injection

value: fibroblasts

value: intraductal injection lenti-cre (T=12 weeks)


title: Progeny 1 of cross 2121, high-bruising group, biol rep 2

value: mechanical impact (bruising)


title: Person D_CD4_IFNg_YM155, 24h

value: IFNg

value: 10 ng/ml YM155

value: D


title: SAN, Control, H3K4me3

city: Houston

first: Jun

last: Wang

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

data_processing:
The paired-end FASTQ format raw reads were aligned to mm10 by Bowtie2 using parameters “--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”, then the duplicates were removed by Picard, and the low-quality mapped reads were filtered by Samtools with the minimum quality score of 30.
To construct the UCSC visualization tracks, we converted alignment files into bigwig and bedgraph format with bamCoverage of deeptools
Then SEACR was used to call peaks with “stringent” and “norm” mode, the IgG alignment file was used as the control data.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

source_name: sinoatrial node

extract_protocol:
Nuclei from SAN tissues were incubated with concanavalin A (Con A)-coated magnetic beads (Bangs Laboratories, BP531) at room temperature for 10 min to immobilized nucleus on the Con A-coated magnetic beads. The bead-bound nuclei were then incubated with anti-H3K4me3 (Active Motif, 39159, 1:100) and anti-Yap1 (Novus, NB110-58358, 1:50) antibodies separately overnight at 4oC with rotation. Guinea pig anti-rabbit second antibody (Antibodies-Online, ABIN101961, 1:100) was diluted in 50 mL of wash buffer, and added into the nucleus to incubate for 30 min at room temperature. The pA-Tn5 adapter complex was diluted 1:200in 300-buffer and incubated with nucleus at room temperature for 1 h. Nucleus were then resuspended in tagmentation buffer at 37oC for 1 h for DNA fragmentation. After 1 h, 0.5M EDTA, 10%SDS, and 20mg/mL Proteinase K were added to terminate tagmentation and incubate for 10 min at 70oC. DNA was then purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation and dissolve in 21 μL 1 mM Tris-HCl at pH 8 and 0.1 mM EDTA.
The libraries were prepared by add 2 uL of 10uM barcoded i5 primer, 2 uL of 10uM uniquely barcoded i7 primers and 25 uL NEBNext HiFi 2X PCR Master mix (Biolabs, M0541L), and PCR was performed according to the conditions in the protocol.  AMPure XP beads (Beckman Coulter, A63880) were used for DNA purification. Libraries were sequenced on NextSeq 550 (Illumina, USA) at UTHealth Cancer Genomics Center, and 75-bp paired-end reads were generated. Fastp software was used to remove adaptor and low-quality reads. All reads produced by CUT&Tag of H3K4me3 were aligned to the hg19 human genome using BWA (Burrows-Wheeler Aligner). MACS2 was used for peak calling. Genes with a peak within 3 kb of the transcription start site (TSS) were considered target genes. An area of 6 kb surrounding each TSS was selected to get CUT&Tag profiles of H3K4ac using deepTools software. Annotation of peaks was performed using ChIPseeker.

value: sinoatrial node

tag: chip antibody

value: H3K4me3  (Active Motif, 39159)

value: Control


title: 090421_PY02_PGC

value: Male

value: 13 days postpartum


title: Person A_CD4_IFNg_YM155, 24h

value: A


title: 140421_PY01_Somatic

value: Somatic

value: 7 days postpartum

value: GFP (SSEA1) negative


title: Person B_CD4_IFNg_YM155, 24h

value: B


title: SAN, Control, IgG (No antibody)

value: anti-rabbit-IgG antibody (Millipore, 12370)


title: Person D_CD4_IFNg, 24h

value: 0 ng/ml YM155


title: 110822_PY01_PGC

value: PGC

value: 12 days postpartum

value: GFP (SSEA1) sorted


title: rrb-1::degron; eft-3p::tir-1, 1 mM auxin, replicate 1

value: Whole animal

value: rrb-1::degron; eft-3p::tir-1

value: 1 mM auxin


title: 140421_PY01_PGC


title: rrb-1::degron, 1 mM auxin, replicate 4


title: SAN, Lat1/2 CKO, Yap

value: sinoatrial node

value: Lat1/2 CKO


title: Person B_CD4_IFNg, 24h

value: IFNg


title: SAN, Control, Yap

value: Control


title: TMD8 expressing BTK C481R cells, ibrutinib, rep2

city: 北京市

first: Hongwei

last: Yuan

state: 北京市

address: 北京市, 昌平区, 北京生命科学研究所

country: China

institute: National Institute of Biological Sciences, Beijing

description:
cell proliferration and differentiation
C481R_ibrutinib_rep2

data_processing:
Sequencing reads were aligned to the Homo sapiens GRCh38 reference transcriptome using Botwie2 followed by gene-level quantification with RSEM
Differential gene expression analyses were performed with DESeq2 with the following cutoff: absolute log2-transformed fold change greater than 2 and P value less than 0.01.
Volcano plot and heatmap were rendered in R.
Gene ontology analysis of differentially expressed genes was performed with clusterProfiler.
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: TMD8 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 2 mM L-glutamine in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated from  cultured cells using TRNzol (Tiangen).
RNA-seq library construction and sequencing were performed by Berry Genomics (Berry Genomics, Beijing, China).

treatment_protocol: Cells were treated with DMSO or 10 nM ibrutinib for 24 hours

value: Human diffuse large B cell lymphoma cell

value: 10 nM ibrutinib for 24 hours


title: rrb-1::degron, 1 mM auxin, replicate 2


title: rrb-1::degron; eft-3p::tir-1, 1 mM auxin, replicate 2


title: PD-L1 knock-out sample

city: Hong Kong

first: Shihui

last: ZHANG

address: Science and Technology W Ave

institute: Centre for Translational Stem Cell Biology Limited

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hEPSE

extract_protocol:
The wild type and PD-L1-/- hPSC lines followed the macrophage differentiation . All cells were collected and resuspended in FACS buffer. Cells were stained by CD11b-APC-Cy7 and CD45-PE. After staining, cells were washed and resuspended in FACS buffer with DAPI. Cells were sorted using Fusion Flow Cytometer (BD Bioscience). DAPI-negative cells were sorted for Single-cell RNA-seq with the support of the Centre for PanorOmic Sciences (CPOS).
the single-cell RNA-seq library was constructed and performed by Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1. Illumina Novaseq 6000 for Pair-End sequencing services was used and the final data output was 206.2 for PD-L1-/-  and 213.9G for wild type.

value: hEPSC

value: PD-L1 knock-out

tag: age

value: Day 25


title: wild type sample

description: 10x Genomics

source_name: hEPSC

value: wild type


title: Person 4_CD4_IFNg_YM155

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells, culture activated with anti-CD3, 72h total

value: 10 ng/ml YM155

value: D


title: TMD8 expressing BTK C481R cells, DMSO, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481R_DMSO_rep2

value: DMSO


title: rrb-1::degron, 1 mM auxin, replicate 1


title: Person 3_CD4_IFNg_YM155

value: C


title: TMD8 expressing BTK C481Y cells, ibrutinib, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481Y_ibrutinib_rep2


title: TMD8 expressing BTK C481Y cells, DMSO, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481Y_DMSO_rep2


title: rpoa-2::degron; eft-3p::tir-1, 1 mM auxin, replicate 3

value: Whole animal

value: rpoa-2::degron; eft-3p::tir-1


title: Person 2_CD4_IFNg_YM155

value: B


title: Person C_CD4_IFNg, 24h

value: 0 ng/ml YM155


title: rpoa-2::degron; eft-3p::tir-1, 1 mM auxin, replicate 2

value: 1 mM auxin


title: rrb-1::degron, 1 mM auxin, replicate 3


title: Person 1_CD4_IFNg_YM155

value: IFNg

value: A


title: rpoa-2::degron; eft-3p::tir-1, 1 mM auxin, replicate 1


title: TMD8 expressing BTK C481F cells, DMSO, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481F_DMSO_rep2

value: Human diffuse large B cell lymphoma cell


title: Person 3_CD4_IFNg


title: TMD8 expressing BTK C481S cells, ibrutinib, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481S_ibrutinib_rep2

value: 10 nM ibrutinib for 24 hours


title: Person A_CD4_IFNg, 24h


title: Person 2_CD4_IFNg


title: chondrocytes, Sirt6 KO2

city: Nanjing

first: Mingliang

last: Ji

state: Jiangsu

address: Dingjiaqiao Road 87

institute: Zhongda Hospital,school of medicine, southeast university

data_processing:
The Fastq format file contains the sequence of reads and the sequencing quality of base.
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Assembly: hg19
Supplementary files format and content: raw counts

organism: Mus

source_name: knee cartilage

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

value: knee cartilage

value: chondrocytes

value: Sirt6 cKO


title: rpoa-2::degron, 1 mM auxin, replicate 3


title: chondrocytes, Sirt6 KO3


title: Person 1_CD4_IFNg


title: TMD8 expressing BTK C481S cells, DMSO, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481S_DMSO_rep2


title: chondrocytes, Sirt6 KO1


title: rpoa-2::degron, 1 mM auxin, replicate 2


title: chondrocytes, NC3

value: wild type


title: TMD8 parental cells, ibrutinib, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
parental_ibrutinib_rep2

value: WT


title: RA patient 27_CD4

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells,

treatment_protocol: culture activated with anti-CD3, 48h total

tag: cell subtype


title: rpoa-2::degron, 1 mM auxin, replicate 1


title: rpoa-2::degron; eft-3p::tir-1, 1 mM auxin, replicate 4


title: TMD8 parental cells, DMSO, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
parental_DMSO_rep2

tag: cell type


title: chondrocytes, NC2


title: RA patient 26_CD4


title: TMD8 expressing BTK C481F cells, ibrutinib, rep2

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481F_ibrutinib_rep2


title: TMD8 expressing BTK C481R cells, ibrutinib, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481R_ibrutinib_rep1


title: rpoa-2::degron, 1 mM auxin, replicate 4

tag: developmental stage


title: TMD8 expressing BTK C481R cells, DMSO, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481R_DMSO_rep1

tag: treatment


title: degron::GFP::rpoa-2; eft-3p::TIR1, embryo, +IAA, 24h_R2

first: Qiuxia

last: Zhao

state: Texas

address: 2415 Speedway

data_processing:
Adapter removal (Truseq HT adapters) and genome mapping (WBcel235) and assignment to protein coding genes were accomplished by using NextFlow preprocessing pipeline, Riboflow.
The raw reads per gene were extracted from the output ribo file using RiboR.
These reads were then analyzed for significant differences with and without auxin using Deseq2 analysis.
Assembly: WBcel235
Supplementary files format and content: CSV file includes transcript counts for each Sample

source_name: whole worm

growth_protocol: Animals were grew at 16 ˚C.

extract_protocol:
RNA was extracted using Trizol. rRNA depetion was performed with Rnase H.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Put synchronized eggs on without or with Auxin (1 mM IAA) NGM plates.

value: whole worm

value: degron::GFP::rpoa-2; eft-3p::TIR1

value: embryos, +Auxin (1 mM), 24h


title: chondrocytes, NC1


title: Person 4_CD4_IFNg

value: D


title: degron::GFP::rpoa-2; eft-3p::TIR1, embryo, +IAA, 24h_R1


title: RA patient 24_CD4


title: RA patient 25_CD4


title: degron::GFP::rpoa-2; col-10p::TIR1, embryo, +IAA, 24h_R3

value: degron::GFP::rpoa-2; col-10p::TIR1


title: RA patient 22_CD4


title: degron::GFP::rpoa-2; col-10p::TIR1, embryo, +IAA, 24h_R2


title: TMD8 expressing BTK C481Y cells, DMSO, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481Y_DMSO_rep1

value: DMSO


title: degron::GFP::rpoa-2; col-10p::TIR1, embryo, +IAA, 24h_R1


title: TMD8 expressing BTK C481F cells, ibrutinib, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481F_ibrutinib_rep1


title: RA patient 21_CD4


title: sample_18, patient_16

type: RNA

city: Munich

first: Carolin

last: Prexler

address: Kölner Platz 1, Haus 11

department: School of Medicine and Health, Department of Pediatrics

country: Germany

institute: Technical University of Munich, TUM University Hospital

description: Gene expression data from sample_18 (patient_16)

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: GCS 3000 7G scanner (Affymetrix) using the standard Affymetrix protocol.

data_processing: RMA normalization using R/Bioconductor based on brainarray custom cdf version 24.0.0 (hugene10st_Hs_ENTREZG).

label: biotin

source_name: Ewing sarcoma

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

extract_protocol: Total RNA was isolated using the RNeasy RNA isolation kit according to the manufacturer's instructions.

value: Ewing sarcoma tumor

tag: Sex

value: female

tag: genetics

value: Relapse

value: Metastasis

tag: therapy

value: Under therapy

value: PET-CT

tag: suvmax


title: sample_19, patient_17

description: Gene expression data from sample_19 (patient_17)

tag: tissue

value: Tumor


title: degron::GFP::rpoa-2, embryo, -IAA, 24h Control 2_R2

tag: genotype

value: embryos, no Auxin, 24h


title: RA patient 20_CD4


title: TMD8 expressing BTK C481F cells, DMSO, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481F_DMSO_rep1

value: Human diffuse large B cell lymphoma cell


title: sample_17, patient_15

description: Gene expression data from sample_17 (patient_15)

value: male

value: Primary Disease

value: Untreated


title: TMD8 expressing BTK C481S cells, ibrutinib, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481S_ibrutinib_rep1

value: 10 nM ibrutinib for 24 hours


title: RA patient 19_CD4


title: degron::GFP::rpoa-2, embryo, -IAA, 24h Control 2_R1

value: whole worm


title: sample_16, patient_14

description: Gene expression data from sample_16 (patient_14)


title: degron::GFP::rpoa-2, embryo, -IAA, 18h Control 1_R2

value: embryos, no Auxin, 18h


title: TMD8 expressing BTK C481Y cells, ibrutinib, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481Y_ibrutinib_rep1


title: TMD8 expressing BTK C481S cells, DMSO, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
C481S_DMSO_rep1


title: RA patient 17_CD4


title: TMD8 parental cells, ibrutinib, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
parental_ibrutinib_rep1

value: WT


title: RA patient 16_CD4


title: TMD8 parental cells, DMSO, rep1

address: 北京市, 昌平区, 北京生命科学研究所

description:
cell proliferration and differentiation
parental_DMSO_rep1

value: DMSO


title: degron::GFP::rpoa-2, embryo, -IAA, 18h Control 1_R1


title: RA patient 15_CD4


title: Wild-type_1_footprint

city: Berkeley

first: Gloria

middle: Ann

last: Brar

state: CA

address: 628 Barker Hall

department: MCB

institute: UC Berkeley

description: ribosome protected fragment

data_processing:
adaptor was trimmed from reads
reads were aligned to genome using bowtie2 excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution.
reads per ORF were counted and RPKMs were calculated
Assembly: sk1_revised_100331 published in Brar et. al, Science, 2012, and eisenberg et al., cell systems 2020)
Supplementary files format and content: ribosome footprint RPKMs for each ORF quantified, two biological replicates for each genotype are included

organism: Saccharomyces cerevisiae

growth_protocol: cells were grown as in Powers et al., 2022, 6h after transfer to SPO media samples were collected and flash frozen

extract_protocol:
cells were mixermilled with frozen buffer described in Powers et al., 2022
as described in Brar et al., 2012 except linker ligation was used instead of poly a tailing
ribosome profiling and mrna-seq

treatment_protocol: cells were treated with 100uM cycloheximide for 30s prior to filtering and flash freezing

value: Wild type

value: cells were transferred to sporulation media to induce sporulation then collected 6h post transfer


title: Wild-type_2_footprint

description: ribosome protected fragment


title: oeDAZL_rep2

city: BEIJING

first: XIAOYU

last: FENG

state: BEIJING

address: QINGHUAYUAN street，HAIDIAN distribute

institute: Tsinghua University

data_processing:
For RNA-seq data,  sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters  -q 25 --phred33 --stringency 3 --length 120. For miRNA-seq  sequenced reads were treated by Cutadapt (v1.18) with parameters -j 16  -a AAAAAAAAAA -u 3 --discard-untrimmed -m 15.
For RNA-seq data,reads were mapped to hg38 whole genome using Hisat2 (v2.1.0) with default parameters. For miRNA-seq, reads were mapped to  mirBase using bowtie  (1.0.0) with default parameters.
For RNA-seq, gene count and TPM value were calculated by Stringtie (2.1.4).
Assembly: hg38
Supplementary files format and content: For RNA-seq, tab-delimited text files include TPM values for each Sample .
Supplementary files format and content: For miRNA-seq, tab-delimited text files include counts for each Sample .

extract_protocol:
Total RNA was extracted using the TRIzol® Reagent (Life Technologies).
For RNA-seq, libraries were constructed by berrygenomic. For miRNA-seq, libraries were constructed  using SMARTer® smRNA-Seq Kit for Illumina (635030, TAKARA).

value: hPGCLCs derived from hESCs

value: oeDAZL


title: RA patient 18_CD4


title: dbp1∆_2_footprint

description: ribosome protected fragment


title: sample_11, patient_10

description: Gene expression data from sample_11 (patient_10)

value: Ewing sarcoma tumor

value: female

value: Relapse

value: Metastasis


title: oeDAZL_rep1


title: sample_12, patient_11

description: Gene expression data from sample_12 (patient_11)

value: PET-CT


title: RA patient 14_CD4


title: sample_14, patient_13

description: Gene expression data from sample_14 (patient_13)


title: sample_13, patient_12

description: Gene expression data from sample_13 (patient_12)

value: male

value: EWS-ERG

value: Under therapy

value: PET-MR


title: RA patient 13_CD4


title: Normal_rep2

value: SD cells derived from hESCs

value: wt

value: spontaneous differentiated


title: RA patient 12_CD4


title: sample_15, patient_12

description: Gene expression data from sample_15 (patient_12)

value: Primary Disease


title: Normal_rep1


title: RA patient 11_CD4


title: RNA-Seq Scaffolds DF MP08

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to Oryctolagus cuniculus (rabbit) genome (oryCun2 ) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against gene transcripts annotated by Ensembl (OryCun2.0.98)
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: oryCun2
Supplementary files format and content: Text; First colum: Gene ID; columns thereafter: expresion values (log2(RPKM+1)+0.0001) for each sample

organism: Oryctolagus cuniculus

source_name: rabbit infrapatellar fat pad derived stem cells (IPFSCs)

extract_protocol:
Total RNAs were isolated by using Trizol (Invitrogen) and purified by using an RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer’s instructions.
RNA-Seq library were prepared by using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) following manufacturer’s instructions.

tag: strain

value: New Zealand White (NZW)

value: IPFSCs grown on dECM deposited by human dermal fibroblasts (DFs), incubated for 21 days in a pellet culture system with chondrogenic induction medium


title: RNA-Seq Scaffolds USC MP10

value: infrapatellar fat pad derived stem cells (IPFSCs)

value: IPFSCs grown on dECM deposited by human urine stem cells (USCs), incubated for 21 days in a pellet culture system with chondrogenic induction medium


title: RNA-Seq Scaffolds SDSC MP09

value: IPFSCs grown on dECM deposited by human synovium-derived stem cells (SDSCs), incubated for 21 days in a pellet culture system with chondrogenic induction medium


title: RA patient 10_CD4


title: RNA-Seq Scaffolds ASC MP07

value: IPFSCs grown on decellularized extracellular matrix (dECM) deposited by human adipose stem cells (ASCs), incubated for 21 days in a pellet culture system with chondrogenic induction medium


title: dbp1∆_1_footprint

description: ribosome protected fragment

value: cells were transferred to sporulation media to induce sporulation then collected 6h post transfer


title: RA patient 09_CD4


title: RNA-Seq Scaffolds PL MP06

value: IPFSCs grown on tissue culture plastic, incubated for 21 days in a pellet culture system with chondrogenic induction medium


title: RA patient 08_CD4


title: RNA-Seq Cells USC MP05

value: IPFSCs grown on dECM deposited by human urine stem cells (USCs)


title: RA patient 05_CD4


title: RNA-Seq Cells SDSC MP04

value: IPFSCs grown on dECM deposited by human synovium-derived stem cells (SDSCs)


title: RA patient 04_CD4


title: RA patient 03_CD4


title: sample_10, patient_9

description: Gene expression data from sample_10 (patient_9)

value: Ewing sarcoma tumor

value: female

value: Relapse

value: Tumor

value: Untreated

value: PET-CT


title: small intestine crypt 2

city: Beijing

first: Zhimin

last: Jiang

address: Yuanmingyuang west road 2

institute: Chinese Agricultural University

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
We used SOAPnuke(v1.5.2) to filter the raw reads, the filtering rules were as follows: 1) Removed reads containing adapters, 2) Removed reads with N ratio greater than 5%, 3) Removed low-quality reads (the number of bases with quality value Q<=15 accounts for more than 20% of the entire read).
We used CIRI(v2.0.5) and find_circ(v1.2) to predict circRNA, and integrate the results of the two software according to the start and end positions of circRNA. CircRNAs that satisfied both starting and ending positions within 10 bases before and after were merged into one class. The known circRNAs were identified according to the circBase database, and the source genes of the circRNAs were determined according to the location information of the reference genome and functional annotations were performed on the source genes (3 error bases were allowed for both the start and end positions).
We calculated the expression of circRNA according to the number of back-spliced reads aligned to both ends of the circRNA. Since two software CIRI and find_circ were used for prediction, the final number of back-spliced reads was the average of the prediction results of the two softwares. In this study, RPM (RPM=num of back-spliced reads mapped A gene * 10^6/Total number of back-spliced reads) was used to normalize each sample. Then DEGseq software was used to detect differential circRNAs and P-values were corrected to Q-value by two strategies, Q value≤ 0.001 and the absolute value of Log2FoldChange ≥ 1 was the default threshold to judge the significance of expression difference.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene reads  for each gene and each sample.

source_name: small intestine

extract_protocol:
RNA was harvested using RNAprep Pure Micro Kit (Tiangen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using MGIEasy RNA Library Prep Kit V3.0 (MGI-tech) following manufacturer's protocols.

value: small intestine

value: small Intestinal stem cells

value: wild-type


title: RNA-Seq Cells ASC MP02

value: New Zealand White (NZW)

value: infrapatellar fat pad derived stem cells (IPFSCs)

value: IPFSCs grown on decellularized extracellular matrix (dECM) deposited by human adipose stem cells (ASCs)


title: sample_9, patient_8

description: Gene expression data from sample_9 (patient_8)

value: male

value: Primary Disease

value: PET-MR


title: small intestine crypt 1


title: RA patient 02_CD4


title: RNA-Seq Cells PL MP01

value: IPFSCs grown on tissue culture plastic


title: sample_7, patient_4

description: Gene expression data from sample_7 (patient_4)

value: Metastasis

value: Under therapy


title: RA patient 01_CD4


title: sample_8, patient_7

description: Gene expression data from sample_8 (patient_7)

value: Ewing sarcoma tumor

value: female


title: sample_6, patient_6

description: Gene expression data from sample_6 (patient_6)

value: Relapse


title: RNA-Seq Cells DF MP03

value: IPFSCs grown on dECM deposited by human dermal fibroblasts (DFs)


title: sample_5, patient_5

description: Gene expression data from sample_5 (patient_5)

value: PET-CT


title: sample_2, patient_2

description: Gene expression data from sample_2 (patient_2)


title: sample_4, patient_4

description: Gene expression data from sample_4 (patient_4)

value: Untreated


title: sepsis liver, replicate 9

status: Public on Nov 28 2022

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Reads were pre-processed with Trimmomatic v0.39 to trim adapters (standard settings) and low quality bases with a sliding window approach (width 5, quality cut-off 20)
Processed reads were mapped to the Sscrofa11.1 reference genome using the hisat2 alignerwith standard settings
reads counts were obtained using the featurecounts software
read count normalization and differential gene expression was obtained using R software and the DESeq2 libarary
Assembly: Sscrofa11.1
Supplementary files format and content: tab delimied text file with raw read counts (as obtained by featurecount) per sample

organism: Sus scrofa

source_name: liver

extract_protocol:
Liver samples were isolated and stored in RNALater (Ambion). RNA was isolated using the Aurum total RNA mini kit (Biorad)
RNA libraries for RNA-seq were prepared using the illumina stranded Library Prep Kit following manufacturer's protocols.

treatment_protocol: Pigs were operated on with or without induction of sepsis (sham controls & sespsis), and treated further acoring to the protocol described in Garcia et al. (Crit Care 2022, 26, 281)

value: liver

value: abdominal sepsis model


title: sepsis liver, replicate 7


title: sham liver, replicate 3

value: sham surgery


title: sham liver, replicate 1


title: sepsis liver, replicate 1


title: sample_3, patient_3

description: Gene expression data from sample_3 (patient_3)


title: sepsis liver, replicate 4


title: sham liver, replicate 2


title: sepsis liver, replicate 8


title: sepsis liver, replicate 5


title: sepsis liver, replicate 6


title: sepsis liver, replicate 2


title: sample_1, patient_1

description: Gene expression data from sample_1 (patient_1)

value: Tumor


title: sepsis liver, replicate 3


title: iPS microglia_IFNg_A11_B8

city: Cambridge

first: William

last: Ralvenius

address: 43 Vassar St

institute: MIT

data_processing:
Gene expression was quantified using salmon version 1.3.0 (Patro et al. 2017) using a transcriptome prepared from the human hg38 primary genome assembly using the ensembl version 101 annotation.  The resulting counts were summarized to the gene level using R version 4.1.0 (R Core Team 2021) running tximport version 1.20.0 (Soneson, Love, and Robinson 2015) and the transcripts per million (tpm) values with a +1 offset were transformed to log2 space.
SAMPLES 1-10 were processed together with DPBS (1% DMSO) as control. SAMPLES 11-25 were processed together with DPBS (1% DMSO) as control. SAMPLES 26-34 were processed separately with DPBS (1% DMSO) as control.
Assembly: hg38 with ensembl v101 annotation
Supplementary files format and content: csv files for DEGs with adjsuted p value (apeglm)

source_name: human iPSC

growth_protocol: iPS microglia were maintained as described in McQuade et al. 2018, ref: https://molecularneurodegeneration.biomedcentral.com/articles/10.1186/s13024-018-0297-x except no CD200, TGFβ or fractalkine was added to the medium. Cells were treated on day 45 in culture for all conditions.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) after scraping of wells. 100 000 cells were plated per well in a tissue culture treated 12 well plate.
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit V2 (Pico) following manufacturer's protocols.

treatment_protocol:
Negative control (vehicle) was DPBS, 1 % DMSO. Pro-inflammatory molecule only was either LPS (25ng/mL) + DPBS (1% DMSO) or TGFβ (25 ng/mL) + DPBS (1% DMSO) or TNFɑ (25 ng/mL) + DPBS (1% DMSO) or IFNγ (25 ng/mL) + DPBS (1% DMSO)
Proinflammatory molecule and A11 was either LPS (25 ng/µL) + A11 (20 nM, in DPBS, 1 % DMSO) or TGFβ (25 ng/µL) + A11 (20 nM, in DPBS, 1 % DMSO) or TNFɑ (25 ng/µL) + A11 (20 nM, in DPBS, 1 % DMSO) or IFNγ (25 ng/µL) + A11 (20 nM, in DPBS, 1 % DMSO)

value: human iPSC

value: Human iPS microglia

tag: catalog

value: Coriell #AG09173 ( female, Age 75)

value: IFNBeta (25 ng/microL) + A11 (20 nM, in DPBS, 1 percent DMSO)

tag: time

value: 48 hours


title: iPS microglia_IFNg_veh_B6

tag: cell line

value: IFNBeta (25 ng/mL) + DPBS (1percent DMSO)


title: iPS microglia_IFNg_A11_B7


title: iPS microglia_IFNg_A11_B9


title: iPS microglia_IFNg_veh_B4


title: iPS microglia_IFNg_veh_B5


title: iPS microglia_DPBS_C2

value: DPBS, 1 percent DMSO


title: iPS microglia_DPBS_C1


title: iPS microglia_DPBS_C3


title: OA3.Ts cells, BTV-1 Y863 strain infected for 24 h, 3

city: Kunming

first: Zhuoran

last: Li

state: Yunnan

address: Fengyu Road

department: Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory

institute: Yunnan Animal Science and Veterinary Institute

data_processing:
Fastp (v0.14.1) was used to remove the mRNA, lncRNA and circRNA reads that contained adaptor contamination, low quality bases and undetermined bases, and verify the sequence quality.
Hisat2 (v2.0.4) for mRNA, as well as Bowtie2 (v2.2.5) and Tophat2 (v2.0.13) for lncRNA were used to map reads to the genome of Ovis aries (GCA_000298735.1).
The mapped mRNA and lncRNA reads of each sample were assembled with StringTie (v1.3.0) respectively, and then the mRNA or lncRNA transcripts from all samples were merged to reconstruct a comprehensive transcript profile using GffCompare.
Subsequently, transcripts annotated as known mRNAs, known lncRNAs, and less than 200 nt in length were discarded. Coding Potential Calculator (CPC) software (v0.9-r2) and Coding-Non-Coding Index (CNCI) software (v2.0) were unutilized to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 was removed. The remaining transcripts with class code (l, j, o, u, and x) were considered as novel lncRNAs
Bowtie2 (v2.2.5) and Tophat2 (v2.0.13) for circRNA were used to map reads to the Ovis aries genome (GCA_000298735.1). The remaining unmapped circRNA reads were further mapped to genome using Tophat-Fusion (v2.0.12).
As for mapped circRNA reads, they firstly were de novo assembled to circular using CIRCexploer (v1.1.10) and CircRNA Identifier (CIRI) (v2); then, back splicing reads were identified in unmapped reads by Tophat-Fusion (v2.0.12) and CIRCexploer (v1.1.10).
Assembly: Ovis aries (GCA_000298735.1)
Supplementary files format and content: tab-delimited text files include count, RPKM values for each Sample

organism: Ovis aries

source_name: embryonic testicular

growth_protocol: OA3.Ts cells were maintained in F12: DMEM =1: 1 medium supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA from each sample was extracted with TRIzol reagent (Invitrogen, USA). In order to construct mRNA library, poly(A) RNA was purified for two rounds from 2 μg total RNA using Dynabeads Oligo(dT)25-61005 (Thermo Fisher, USA). Approximately 2 μg of total RNA was used to remove ribosomal RNA according to the manuscript of the Ribo-Zero Gold Kit (Epicentre Biotechnologies, USA) to construct lncRNA or circRNA library.
The poly(A) RNA and the remaining RNA after ribosomal RNA removal were fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, USA). The cleaved RNA fragments were reverse-transcribed into cDNA by SuperScript Ⅱ Reverse Transcriptase (Invitrogen), which were subsequently used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase Ⅰ (NEB), RNase H (NEB) and dUTP Solution (Thermo Fisher). An A-base was then added to the blunt ends of each strand, followed by ligation of indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters were ligated to the fragments, and size selection was performed with AMPure XP beads (Beckman Coulter, USA). After the heat-labile UDG enzyme (NEB) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR. The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: OA3.Ts cells were infected with BTV-1 Y863 strain with a multiplicity of infection (MOI) of 1. After 1 h of incubation, the supernatants were discarded. OA3.Ts cells were then maintained with F12: DMEM =1: 1 medium supplemented with 1% FBS for 24 h. The uninfected OA3.Ts cells served as the mock-infected controls.

value: embryonic testicular

value: embryonic testicular cells

value: BTV-1 Y863 strain infected for 24 h


title: OA3.Ts cells, BTV-1 Y863 strain infected for 24 h, 2


title: OA3.Ts cells, mock-infected, 2

value: mock-infected


title: OA3.Ts cells, mock-infected, 3


title: OA3.Ts cells, BTV-1 Y863 strain infected for 24 h, 1


title: OA3.Ts cells, mock-infected, 1


title: iPS microglia_TNFa_A11_B9

value: TNFɑ (25 ng/microL) + A11 (20 nM, in DPBS, 1 percent DMSO)


title: iPS microglia_TGFb_A11_B9

value: TGFβ (25 ng/microL) + A11 (20 nM, in DPBS, 1 percent DMSO)


title: iPS microglia_TNFa_veh_B6

value: TNFɑ (25 ng/mL) + DPBS (1percent DMSO)


title: iPS microglia_TNFa_A11_B7


title: iPS microglia_TNFa_veh_B4


title: iPS microglia_TGFb_veh_B4

value: TGFβ (25 ng/mL) + DPBS (1percent DMSO)


title: iPS microglia_TNFa_veh_B5


title: iPS microglia_TGFb_veh_B5


title: iPS microglia_DPBS_B3


title: iPS microglia_TGFb_A11_B8


title: iPS microglia_TGFb_veh_B6


title: iPS microglia_TNFa_A11_B8


title: iPS microglia_DPBS_B2


title: iPS microglia_TGFb_A11_B7


title: iPS microglia_DPBS_B1


title: iPS microglia_LPS_A11_A3

value: LPS (25 ng/microL) + A11 (20 nM, in DPBS, 1 percent DMSO)


title: iPS microglia_LPS_A11_A2


title: iPS microglia_LPS_A11_A1


title: WB3

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

data_processing:
Partek® Flow® 8.0
Bases were trimmed on quality score=20. Adaptors were also trimmed.
Filter BAM files with minimal mapping quality=20.
Alignment usign STAR - 2.7.3a to Solanum lycopersicum SL3.0 assembly (NCBI genome assembly ID 393272)
Quantification to transcriptome performed using Partek E/M algorithm.
Assembly: Solanum lycopersicum SL3.0 assembly (NCBI genome assembly ID 393272)
Supplementary files format and content: Sobol_tomato_NormRPKM_SolycID

organism: Solanum lycopersicum

source_name: tomato plant

growth_protocol: CRISPR/Cas9-generated tomato BSK830 mutant lines were impaired in ROS accumulation induced by the flg22 and flgII-28 flagellin epitopes. In addition, in wild-type plants the flagellin deficient Pseudomonas syringae pv. tomato (Pst) strain DfliC developed larger populations than wild-type Pst bacteria, whereas in BSK830 mutants Pst wild-type and DfliC bacteria displayed a similar growth.

extract_protocol:
Total RNA was extracted with the RNeasy Plant Mini Kit (QIAGEN) followed by mRNA libraries construction
RNA-Seq cDNA libraries were prepared from the RNA samples using the NEBNext Ultra™ II mRNA Library Prep Kit for Illumina and then PCR amplified using NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions (New England Biolabs).

treatment_protocol: Total RNA was isolated with the RNeasy Plant Mini Kit (QIAGEN) from leaves of wild-type and bsk830-1 tomato plants infected by vacuum with a suspension of P. fluorescens or mock-inoculated (three biological replicates for each treatment, in total 12 samples collected at 6 h post-inoculation). RNA integrity was evaluated using the 4200 TapeStation System (Agilent Technologies).

value: WT

tag: infection

value: mock


title: iPS microglia_LPS_veh_A3

value: human iPSC

value: Human iPS microglia

value: LPS (25ng/mL) + DPBS (1percent DMSO)


title: MA3

value: bsk830-1 mutant

value: P. fluorescens


title: MB3


title: WB2


title: iPS microglia_LPS_veh_A2

value: Coriell #AG09173 ( female, Age 75)

value: 48 hours


title: iPS microglia_DPBS_A4

value: DPBS, 1 percent DMSO


title: iPS microglia_LPS_veh_A1


title: WA2


title: MB2


title: MB1


title: iPS microglia_DPBS_A3


title: iPS microglia_DPBS_A1


title: WB1


title: iPS microglia_DPBS_A2


title: MA1


title: WA1


title: Keratinocytes_2

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

description: single cell DNA

data_processing:
Alignment of the raw fastq-data with bsmap 2.7 to reference genome.
extraction of coverage and methylation rartios with methratio.py
Assembly: hg19
Supplementary files format and content: bed, modified, col1: cell ID, col2: chrom. Col3: pos begin, col4: pos end, col5: coverage, col6: methylation ratio

source_name: Healthy epidermis

extract_protocol:
A healthy whole human skin biopsy was obtained from the ilioinguinal region of a 62 y/o male donor of fair-skin type. The sample was immersed in MACS Tissue Storage solution (Miltenyi Biotec) immediately after resection and was kept on ice until further processing. The single-cell suspension from the epidermis was obtained using the Epidermis Dissociation Kit for human material (Miltenyi Biotec), and following the manufacturer´s instructions. We then followed the previously published sci-MET protocol (Mulqueen et al., 2018), with important modifications. Hence, cells were then fixed by incubation with 1.5% formaldehyde (without methanol) in 1 mL of PBS for 10 minutes, with gentle shaking. The reaction was stopped by adding 80 µL of 2.5 M glycine followed by 5 minutes incubation on ice. The sample was centrifuged at 550 g for 10 minutes at 4°C to recover fixed cells. Nuclear isolation was performed using the lysis buffer recipe described in (Wysocka et al., 2001) and as described for the single-cell multi-omics dataset. Recovered nuclei were subsequently subjected to nucleosome depletion. To do so, fixed nuclei were resuspended in 800 µl of 1X NEBuffer 2.1 (New England Biolabs) supplemented with 0.3% SDS, and incubated for 30 minutes at 42°C with intense shaking. Then, 200 µL of 10% Triton X-100 were added to the sample, which was incubated for 30 minutes at 42°C with intense shaking. Nuclei were then centrifuged at 500 g for 5 minutes at 4°C and filtered through a 40-µm cell strainer. The nuclear stain TO-PRO™-3 Iodide (1:10,000; Invitrogen) was then added, and we subsequently proceeded to fluorescence-activated nuclei sorting (FANS).
In a first sorting step, we sorted 1,000 nuclei/well into a 96-well plate containing 5 µL of 2X Tagmentation Buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 140 µM PitStop 2 (Sigma-Aldrich), 20% DMF) and 5 µL of nuclear isolation buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 (Sigma-Aldrich), 1X protease inhibitors cocktail). Next, 4 µL of a uniquely indexed transposome were added to each well, and the plate was incubated at 55°C for 30 minutes in a thermocycler for nuclear tagmentation. Importantly, transposomes were built by loading 96 uniquely barcoded cytosine-depleted oligonucleotides (Mulqueen et al., 2018) onto a homemade Tn5 transposase obtained from the European Molecular Biology Laboratory (EMBL; Heidelberg, Germany). See Supplementary Methods for transposome assembly and activity test description. After tagmentation, nuclei from the 96 wells were pooled, mixed, and filtered through a 40-µm cell strainer again. Fresh TO-PRO™-3 Iodide (1:10,000; Invitrogen) was added for the second sorting step.  In this second sorting, we sorted 22 nuclei/well in a full 96-well plate containing 5 µL of Zymo Digestion Reagent (2.5 μL of Zymo M-Digestion Buffer, 2.25 μL of nuclease-free H2O, and 0.25 μL of Proteinase K), following the manufacturer’s instructions of the EZ-96 DNA Methylation-Direct MagPrep Kit (Zymo Research).  Only 10 nuclei were sorted in three wells, where 35 pg of a barcoded-lambda DNA were added as spike-in controls. The plate was incubated for 4 hours at 50°C for nuclear digestion. Bisulfite conversion was then performed by adding 32.5 µL of Zymo CT Conversion Reagent in each well and incubating the plate according to the manufacturer´s instructions (98°C for 8 minutes and 64°C for 3.5 hours). After conversion, bisulfite-converted DNA was desulphonated, washed and recovered following the manufacturer´s instructions. In brief, 5 µL of Zymo M-Binding Beads diluted in 150 µl of Zymo M-Binding Buffer were added to each well, and the plate was incubated for 5 minutes at room temperature for allowing the DNA to attach to the beads. Beads were then washed with 80% ethanol, resuspended in 50 µL of Zymo M-Desulphonation Buffer and incubated at room temperature for 15 minutes. Beads were then washed again in 80% ethanol, and DNA was subsequently eluted in 25 µL of Zymo M-Elution Buffer. Eluted DNA was transferred to a 96-well plate containing 16 µL of nuclease-free H2O, 5 µL of 10X NEBuffer 2.1 (New England Biolabs), 2 µL of 10 mM dNTP mix, and 2 µL of 9-nucleotide random primers(Mulqueen et al., 2018). DNA was subjected to four rounds of linear amplification in a thermocycler by incubating at 95ºC for 45 seconds to achieve denaturation. The plate was quickly placed on ice, and 10 U of Klenow (3’-5’ exo-) polymerase (Biozym Scientific) were added per well. The plate was placed again in the thermocycler for incubation at 4ºC for 5 minutes, followed by incubation at 37ºC for 90 minutes. Importantly, the temperature was increased to 37ºC by 1ºC/15 seconds. In each amplification round, fresh reagents were added to each well (1.25 µL of 4X NEBuffer 2.1(New England Biolabs), 1 µL of 10 µM dNTP mix, and 1 µL of 9-nucleotide random primers(Mulqueen et al., 2018)) as well as 10 U of Klenow (3’-5’ exo-) polymerase (Biozym Scientific). Amplified material was subsequently purified using AMPureXP beads (Beckman Coulter) at a 1.1X volume. DNA was attached to the beads, washed with 80% ethanol, and eluted in 21 µL of EB Buffer (Qiagen). Eluted DNA was added to a 96-well plate containing 25 µL of 2X KAPA HiFi HotStart ReadyMix (Roche), 2 µL of 10 µM i7 index PCR primer, and 2 µL of i5 index PCR primer. Index PCR reaction was performed in a thermocycler by incubating at 95ºC for 2 minutes, then performing 18 cycles at 94ºC for 80 seconds and, finally, incubating at 65ºC for 30 seconds and at 72ºC for 30 seconds. The number of cycles was determined by a qPCR reaction performed with additional wells and could be up to 21 cycles. Libraries were then pooled to achieve a particular cell number and purified using a double-sided size selection step with AMPureXP Beads (0.6X-0.8X; Beckman Coulter) . The library was subsequently quantified with Qubit dsDNA HS Assay Kit (Invitrogen), and fragment size was assessed using D5000 or D1000 ScreenTapes (Agilent Technologies). Paired-end (150 bp) sequencing (100 cycles) was finally performed with a NextSeq550 High-Output (Illumina) system following a custom-made recipe (Read 1: 100 imaged cycles; Index Read 1: 10 imaged cycles; Index Read 2: 11 imaged cycles, 16 dark cycles and 10 imaged cycles).
Sci-MET

value: Healthy epidermis


title: Keratinocytes_3

description: single cell DNA


title: Keratinocytes_1

description: single cell DNA


title: WA3


title: MA2


title: MCF7-AROE, ENZ, biol rep 2

city: Rochester

first: Liewei

state: Minnesota

address: 200 First Street SW

department: Molecular Pharmacology and Experimental Therapeutics department

institute: Mayo Clinic

data_processing:
Filtered reads were aligned to hg38 human reference genome using STAR with average mapping rate of 93%. Raw counts were then called by HTSeq excluding non-unique mapped reads.
Read count extraction and normalization were performed by EdgeR package using R software
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (74134, QIAGEN) per manufacturer’s instructions.
Poly-A enriched RNA library prep and sequencing were done by Mayo Next Gen sequencing cores using illumina truseq2 kit.

treatment_protocol:
MCF7-Tet cells were used to create AR low (no doxycycline) and AR high cells (doxycycline 800ng/ml). Doxycycline was added to cell culture media 1 day before drug treatments.
MCF7 parental and AROE cells were treated with DMSO or Enzalutamide (10µM) for 24 hours.

value: human breast cancer

value: AR overexpression

value: Enzalutamide

value: Day 2


title: G564E-2

city: Gwangju,Korea

first: Jeong-Il

last: Kim

address: Chonnam National University, Gwangju 61186, Korea

department: Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University

country: South Korea

institute: Chonnam national university

description: replicate 2

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC(v0.11.8) & Trimmomatic (v0.39) software
The raw reads were trimmed and quality-filtered before alignment, and those with more than 90 % threshold (Q>30) were used for mapping. B. rapa reference genome was obtained from Ensembl and were used using the TopHat2 software with default parameters
Aligned reads were converted to digital counts using HTseq-count and were analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a 0.05 p-value and a cutoff of two-fold difference in expression.
Assembly: B. rapa reference genome was obtained from Ensembl
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Brassica rapa

source_name: Whole plant

growth_protocol: 2 weeks old B. rapa plants were grown in 1/2 MS (Murashige and Skoog salts, including vitamins) with 0.5% Sucrose.

extract_protocol:
Total RNA was extracted from whole seedling samples using Favoprep Plant Toltal RNA Purification Mini kit (FAVORGEN, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contamination.
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions. Libraries were then sequenced on NovaSeq 6000 system (Macrogen Inc., South Korea)

treatment_protocol: 2weeks old (non-heat treated) plant were grown at LD condition.

tag: cultivar

value: Chiifu

value: AtPHYB mutant


title: G564E-1

description: replicate 1


title: AtPHYB-2

description: replicate 2

value: AtPHYB


title: MCF7, parental, ENZ, biol rep 1

value: WT


title: MCF7, parental, ENZ, biol rep 2


title: G564E-3

description: replicate 3


title: AtPHYB-3

description: replicate 3


title: NT-3

description: replicate 3

value: Wild-type


title: MCF7-AROE, DMSO

value: DMSO


title: AtPHYB-1

description: replicate 1


title: MCF7, AROE, ENZ, Input

description: MCF7-AROE, ENZ

data_processing:
Sequences were aligned to the Human Reference Genome (assembly hg38, UCSC, Dec. 2013) using BWA version 0.7.17.
Enriched regions of the genome were identified by comparing the ChIP samples to input samples using the MACS2 peak caller version 2.1.
Assembly: hg38
Supplementary files format and content: Wig

growth_protocol: EMEM medium with 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit. 10 ng of DNA was used as starting material for input and ip samples.

treatment_protocol: AR expression was induced by doxycycline (800ng/ml) for 24 hours in MCF7-Tet cells. Cells were treated with DMSO or Enzalutamide (10µM) for 2 hours.

tag: chip antibody

value: Rabbit, IgG


title: MCF7-AROE, ENZ, biol rep 1


title: MCF7, AROE, DMSO, ER

description: MCF7-AROE, DMSO

value: ERalpha, Abcam #ab32063


title: NT-2

description: replicate 2


title: MCF7, AROE, DMSO, AR

description: MCF7-AROE, DMSO


title: MCF7, parental, DMSO


title: MCF7, AROE, ENZ, ER

description: MCF7-AROE, ENZ


title: NT-1

description: replicate 1


title: MCF7, AROE, ENZ, AR

description: MCF7-AROE, ENZ


title: MCF7, parental, ENZ, Input

description: MCF7-P, ENZ


title: ECFCLY2_KSHV3

city: Seattle

first: Terri

last: DiMaio

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
perform image analysis and base calling with Illumina's RTA v1.17 Software
demultiplex and generate files in FASTQ format, using Illumina's CASAVA v1.8.2 Software
remove reads that didn't pass Illumina's base call quality threshold
align reads, using TopHat v2.08b ( http://tophat.cbcb.umd.edu/ ) along with Bowtie 1.0.0 ( http://bowtie-bio.sourceforge.net/index.shtml ), using Ensembl's GRCh37 release 70 as the reference genome.
generate counts for each gene using htseq-count v0.5.3p9 (using the intersection-strict overlapping mode)
Assembly: Ensembl's GRCh37 release 70
Supplementary files format and content: tab-delimited text file includes CPM (counts per million reads) for each sample

source_name: whole blood

growth_protocol: Cells were maintained in EGM-2 supplemented with an extra 5% FBS and 1% penicillin/streptomycin/amphotericin

extract_protocol:
RNA was isolated using the RNA isolation kit by Macherey-Nagel. Samples were cleaned and concentrated, where necessary, using Zymogen kit
RNA-seq libraries were generated using Illumina TruSeq RNA Sample Prep Kit v2 following the manufactures protocol.

treatment_protocol: Cells were incubated with KSHV innoculum for 4 hours, then innoculum was removed, and cells were incubated in growth medium for 48 hours.

value: whole blood

value: Endothelial Colony-forming Cells

tag: passage

value: WT KSHV 48hpi


title: ECFCLY2_KSHV1

tag: cell type


title: ECFCLY1_KSHV1


title: ECFCLY1_KSHV2


title: ECFCBL2_KSHV3


title: ECFCLY2_KSHV2


title: MCF7, AROE, DMSO, Input

last: Wang

description: MCF7-AROE, DMSO


title: ECFCBL1_KSHV3


title: ECFCBL2_KSHV1


title: ECFCLY1_KSHV3


title: MCF7, parental, ENZ, ER

description: MCF7-P, ENZ


title: RH3

city: Chicago

first: Anna

last: Di Rienzo

state: IL

department: Human Genetics

institute: University of Chicago

data_processing:
ATAC-seq: Sequence alignment for ATAC-seq performed with bwa (bwa  0.7.17-r1188). Reads were mapped to both the 1,000 genomes Phase2 Reference Genome Sequence (hs37d5) and mitochondrial reads were removed. All ATAC-seq results are given for the build hg19 assembly.
ATAC-seq read filtering performed with samtools (v 1.10)
ATAC-seq peak calling performed with MACS2 (v 2.1.0)
ATAC-seq differential peak calling performed with R packages DiffBind and edgeR
ATAC-seq motif enrichment and peak annotation performed with HOMER (v 4.11.1)
RNA-seq:  sequence alignment and gene expression value estimation was performed using Sequence alignment was performed using a standard pipeline. Briefly, reads were aligned using STAR and read counts performed with RSEM using default settings.
RNA-seq: differential expression analysis was performed with the R package DESeq2
Genome_build: All human samples use genome build hg19.
Supplementary_files_format_and_content: Macs2 narrowPeak file (text)
Supplementary_files_format_and_content: rsem expression levels file (text)

source_name: HAEC

growth_protocol: Paired ATAC-seq and RNA-seq were performed on primary human aortic endothelial cells (HAECs ) in EGM-2 media (Lonza). Triplicate samples of cells cultured for 24 hours in either normoxia (21% O2) or hypoxia (1% O2), were harvested in parallel and processed into ATAC-seq libraries using the Nextera DNA library prep kit (FC-121-1030) or RNA-seq libraries using TruSeq RNA Library Preparation Kit v2, Set B (Illumina, RS-122-2002)

extract_protocol:
harvested in parallel and processed into ATAC-seq libraries using the Nextera DNA library prep kit (FC-121-1030) or RNA-seq libraries using TruSeq RNA Library Preparation Kit v2, Set B (Illumina, RS-122-2002)
samples pooled and run on one lane for RNA and one lane for ATAC

value: Human Aortic Endothelial Cell

value: Aortic endothelium

value: Hypoxia 24 hours


title: RH2

treatment_protocol: Triplicate samples of cells cultured for 24 hours in either normoxia (21% O2) or hypoxia (1% O2)


title: MCF7, parental, DMSO, ER

description: MCF7-P, DMSO

value: human breast cancer


title: MCF7, parental, ENZ, AR

description: MCF7-P, ENZ


title: Cell-BCG

city: Shanghai

first: Li

last: Lin

address: shanghaihuangpu

institute: Shanghai Jiaotong university

description: BCG.CELL

data_processing:
Basecalls performed using CASAVA version 1.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Pick up all miRNA(count>10,Fold change≥20 or ≤0.5)
Genome_build: hg38
Supplementary_files_format_and_content: excel format - enriched peaks

source_name: THP-1 Cell

extract_protocol:
RNA extraction protocol
library construction protocol

value: human monocytic cell line

value: M. bovis bacillus Calmette-Guérin (BCG) infection

tag: sample type

value: cell


title: ECFCBL1_KSHV1

tag: treatment


title: CapHiC_HAEC

data_processing:
Standard promoter capture Hi-C analyses were performed using HOMER. The quality and biological significance of identified interactions was assessed by integrating publicly available RNA-seq  and H3K27Ac Chip-seq. data from the same cell type and examining the correlation between interacting genes, gene activity, and bound transcription factors
Genome_build: All human samples use genome build hg19
Supplementary_files_format_and_content: HOMER analyzeHiC output (text)

growth_protocol: five million HAECs were grown in normoxia for 24 hours in EGM-2 media (Lonza), then harvested and counted.

extract_protocol:
The in situ Hi-C library was hybridized to 81,735 biotinylated 120-bp custom RNA oligomers (CustomArray, Inc. www.customarrayinc.com)) targeting promoter regions (four probes/ RefSeq transcription start sites). After hybridization, post-capture PCR (eight amplification cycles) was performed on the DNA bound to the beads via biotinylated RNA. .
Each library was sequenced on a full lane of an Illumina HiSeq 4000 machine

treatment_protocol: Cells were corsslinked with 1% formaldehyde treatment. Cross-linked chromatin was digested with MboI endonuclease (New England Biolabs, R0147). Subsequently, the restriction fragment overhangs were filled in and the DNA ends were marked with biotin-14-dATP (Life Technologies, 19524-016). The biotin-labeled DNA was sheared and pulled down using Dynabeads MyOne Stretavidin T1 beads (Life Technologies, 65602).

value: Normoxia 24 hours


title: ECFCBL2_KSHV2


title: RH1


title: RN1

value: Normoxia control 24 hours


title: Exo-BCG

description: BCG.EXO

value: exosome


title: H2


title: ECFCBL1_KSHV2


title: FAP inj d1 rep3

city: Toulouse

first: xavier

last: contreras

address: 4bis avenue hubert curien

country: France

institute: RESTORE, INSERM U1301

data_processing:
HiSAT2 alignment
FASTQC for quality control
Feature counts from subread package was used to count feature reads
Deseq2 was used to obtain differentially expressed genes
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized read count values for each Sample

source_name: quadriceps muscle

extract_protocol:
RNA was harvested using Zymo micro kit (Ozyme)
RNA libraries for RNA-seq were prepared by BGI using DNBSeq G-400 kit

value: quadriceps muscle

value: FAP

value: Glycerol injection

value: Day 1


title: RN3


title: Cell-Control

description: Control.CELL

value: un-infected control


title: CD31+CD45+ rep1


title: MCF7, parental, Input

description: MCF7-P, DMSO

value: Rabbit, IgG


title: H3


title: FAP inj d1 rep2


title: RN2


title: FAP inj d1 rep1


title: MCF7, parental, DMSO, AR

description: MCF7-P, DMSO


title: H1


title: Exo-Control

description: Control.EXO


title: FAP rep2

value: NaCl injection


title: N3

value: Human Aortic Endothelial Cell


title: ASC rep3

source_name: subcutaneous adipose tissue

value: subcutaneous adipose tissue

value: ASC


title: N2

value: Aortic endothelium


title: FAP rep1


title: ASC rep2


title: ASC rep1


title: ZM7698_M6_Axillary bud_RNA-seq_rep2

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

data_processing:
Raw reads were trimmed with Trimmomatic v0.334 with default parameters. The remaining reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using HISAT2 v2.0.5. Gene expression values were computed using StringTie v1.3.3b.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: TPM values for each sample

organism: Triticum aestivum

source_name: Triticum aestivum 2-weeks-old seedlings

growth_protocol: 16h light  22°C, 8h dark 19°C

extract_protocol:
total RNA
For each sample, total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit (Illumina, San Diego, CA) following the manufacturer’s instructions.

treatment_protocol: The two tissues of wheat, including axillary buds and shoot apices, were obtained after 2 weeks of growth. The axillary buds were about  1.0 - 2.0 cm.

value: axillary buds

tag: genotype/variation


title: ZM7698_M6_Shoot apex_RNA-seq_rep2

value: shoot apcies


title: ZM7698_M6_Axillary bud_RNA-seq_rep1


title: ZM7698_Axillary bud_RNA-seq_rep1

value: WT


title: ZM7698_Axillary bud_RNA-seq_rep2


title: ZM7698_Shoot apex_RNA-seq_rep1


title: AK58_Axillary bud_RNA-seq_rep2

source_name: Triticum aestivum 6-weeks-old seedlings

treatment_protocol: The three tissues of wheat, including leaves, roots and shoot apices, were obtained after 2 weeks of growth. The 2-week-old seeding were vernalized at 4°C under 16h light/8h dark conditions for 30 days and 1.0 - 2.0 cm axillary buds were obtained from these vernalized seedings.

value: vernalized at 4°C under for 30 days


title: ZM7698_Shoot apex_RNA-seq_rep2


title: AK58_Axillary bud_RNA-seq_rep1


title: AK58_Shoot apex_RNA-seq_rep2


title: N1

value: Normoxia control 24 hours


title: AK58_Shoot apex_RNA-seq_rep1


title: ZM7698_M6_Shoot apex_RNA-seq_rep1


title: Aged, Input, replicate3

city: Brisbane

first: He

last: Huang

state: QUEENSLAND

address: THE UNIVERSITY OF QUEENSLAND, ST LUCIA

country: Australia

institute: The University of Queensland

data_processing:
Sequenced reads were subjected to Trimmomatic (Trimmomatic-0.36) to trim off low quality reads and remove adaptors.
All reads were then aligned against a custom contaminant list to further filter reads mapped to rRNA or Phi X genomes using Sortmerna (version 2.1) or Bowtie2 (version 2.2.7).
Sequenced reads were aligned to mouse genome (mm10) by using the STAR (version 2.5.3a).
Only uniquely mapped reads were selected by Samtools (version 1.3).
Macs2-2.2.1 was used to detect m6A sites.
Peak counts were further generated by Subread (1.6.4) and annotated with Bedtools (2.25.0).
Assembly: mm10

source_name: Hippocampus tissue

extract_protocol:
Total RNA extraction was performed from each individual hippocampal tissue with NucleoZol and NucleoSpin RNA Set (Macherey-Nagel) with rDNase treatment.
Three biological replicates per age group were selected from the pre-validation qPCR assay and subjected to further poly(A)-RNA enrichment using Oligo d(T)25 magnetic beads (NEB).
Approximately 1.4 μg Poly(A)-RNA were chemically fragmented to ~100 nt using NEBNext RNA fragmentation buffer (NEB).
RNA immunoprecipitation with the m6A-specific antibody (cat no. 202 003; Synaptic System) was performed as previously described (Widagdo et al., 2016).
The input and immunoprecipitated RNA were converted to libraries using the SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian (Takara Bio) and their dual combinatorial indexes for multiplexing.

tag: Sex

value: Male

value: Hippocampus tissue

tag: antibody

value: none (input)

tag: age


title: RNA-seq_Young, replicate1

data_processing:
STAR version 2.7.8a was used for building genome indices and mapping.
Adapter trimming was performed using trimgalore version 0.6.6.
consensusDE version 1.8.0 was used for summarizing read counts and differential expression analysis using R version 4.05.
consensusDE simultaneously conducts statistical analysis using edgeR (version 3.32.1) with the additional option to remove unwanted sources of variation with RUV.
Assembly: mm39

extract_protocol:
Total RNA extraction was performed from each individual hippocampal tissue with NucleoZol and NucleoSpin RNA Set (Macherey-Nagel) with rDNase treatment.
libraries were generated using NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB).

tag: tissue


title: Aged, Input, replicate1


title: AK58_Root_RNA-seq_rep1

value: roots


title: Aged, Input, replicate2


title: Aged, IP, replicate1

value: m6A (cat no. 202 003; Synaptic System)


title: RNA-seq_Aged, replicate2


title: Young, IP, replicate1


title: RNA-seq_Aged, replicate3


title: Young, Input, replicate3


title: RNA-seq_Aged, replicate1


title: AK58_Leaf_RNA-seq_rep2

value: leaves


title: Aged, IP, replicate3


title: Young, IP, replicate2


title: RNA-seq_Young, replicate3


title: Aged, IP, replicate2


title: Young, IP, replicate3


title: AK58_Leaf_RNA-seq_rep1


title: Ta-input2

description: control.pks.bed

data_processing:
Library strategy: DAP-seq
Raw reads were trimmed with Trimmomatic v0.36, clean sequencing reads were mapped to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using Bowtie2. Peak calling was performed using MACS2. A black list was first generated by using the control samples as input. Raw peaks were first identified with MACS2 with the following parameter with the following parameter “--keep-dup all --nomodel --extsizes 150”; then split into 150bp bins with 50bp overlapping; bins passed filtering using a reads density cutoff were selected and merged with bedtools with “-d 150”; peaks overlapped with the blacklist peaks, or homologous to plant orgenella DNA (NCBI) were discard and the rest were considered as high-quality binding peaks.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: peak files

extract_protocol: genomic DNA

treatment_protocol: Full length TF was cloned into pIX-Halo vector, the HALO-SPL protein was generated using 500 ng of pIX-HALO-SPL plasmid and the TNT SP6 Coupled Reticulocyte Lysate System (Promega, L4600) according to the manufacturer’s protocol. The reaction was then incubated with 10 μL of Magne-HALO Tag beads (Promega, G7282) for 1 h at 25 °C in 1× PBS with 0.005% Nonidet P-40 (PBST). Bound protein was washed five times with PBST and subsequently treated with DNaseI. The DNA-free HALO-SPL protein was incubated with 500 μg of ultrasonicated genomic DNA library (200~800 bp) for 1 h at 25 °C. The beads were then washed eight times with PBST and incubated with 1μl Tn5 transposomes in 40 μl of tagmentation buffer (10 mM TAPS-NaOH ph 8.0, 5 mM MgCl2) at 55°C for 10 minutes. The DNA were recovered by NEB Monarch™ DNA Cleanup Kit (T1030L) and then amplified using Phusion DNA polymerase for 10-13 cycles. Amplified libraries were purified with AMPure beads to remove primers.


title: Young, Input, replicate1


title: Ta-input

description: control.pks.bed


title: 41AD

data_processing:
Sequence alignment was performed using a standard pipeline. Briefly, reads were aligned using STAR and read counts performed with RSEM using default settings.
Differential expression analyses performed using the r package limma-voom with default settings . All data were processed together, and contrasts made between hypoxia and normoxia for each genotype (WT or KO).
Genome_build: All mouse samples use genome build mm10.
Supplementary_files_format_and_content: rsem expression levels file (text)

extract_protocol:
The following morning, both mice were removed together and euthanized one at a time in a randomly selected order via urethane injection. Mice were rapidly dissected and left kidney, right adrenal gland, left lung, left and right atria, and left and right ventricle were all independently flash frozen in either RLT Plus buffer (kidney, adrenal gland, lung) or Trizol (all heart tissues) and stored at -80C degrees. Once all tissues had been collected from all three pairs of mice, tissues were removed from -80C and homogenized. RNA was extracted one tissue at a time using RNeasy Plus Mini kit (Qiagen, 74134) in a Qiagen Qiacube for all samples stored in RLT buffer and by hand using RNeasy plus mini kit with Qiagen Dnase treatment (RNase-Free DNase Set, cat#79254).
Libraries were constructed using the TruSeq RNA Library Preparation Kit v2, Set B (Illumina, RS-122-2002)
All samples for each organ were pooled and each organ run across one lane of a hiSeq4000

treatment_protocol: At age 9 weeks the mice were placed in pairs, one KO and one WT, into a custom hypobaric hypoxia chamber . The pressure was set to 280-290 mmHg which is equivalent to ~8% O2 and the mice were left overnight (~16.5 hours)

value: Adrenal Gland

tag: genotype

value: musENH5 KO mouse

value: musENH5 Knockout, 16.5 hours hypobaric hypoxia, 8% O2


title: 42AD

value: WT control mouse

value: WT control mouse, 16.5 hours hypobaric hypoxia, 8% O2


title: SPL19B_rep2

value: Magne-HALO Tag beads (Promega, G7282)


title: AK58_Root_RNA-seq_rep2


title: 40AD


title: SPL19B_rep1


title: Young, Input, replicate2


title: 39AD


title: 38AD


title: 37AD


title: 34LG

value: Left Lung


title: SPL18D2


title: SPL18A


title: SPL15D


title: SPL15B


title: 31LG


title: 35LG


title: SPL14B


title: 36LG


title: SPL16D


title: SPL16A


title: SPL15A


title: SPL13B


title: 32LG


title: Water drinking-2nd batch [Water6]

city: Belmont

first: Joy

last: Otten

state: Massachusetts

address: 115 Mill Street

institute: McLean Hospital

data_processing:
Fastq data was obtained from BGI (Hong Kong, China), then  assessed with FastQC (version 0.11.8, Babraham Institute, Cambridge, UK). Salmon (version 0.14.1) was used to first build a transcriptome index using the combined reference transcriptome and non-coding RNAs for Mus musculus (GRCm38/mm10), and then to quantify the RNA-seq reads at the transcript level. The tximport (Bioconductor version 3.12) was used to import the transcript-level abundances generated by Salmon, the estimated counts and the corresponding transcript lengths, and to summarize it into transcript-level and gene-level expression matrices.
Assembly: mm38
Supplementary files format and content: tab-delimited text files with raw counts for each sample

source_name: Brain, Amygdala

extract_protocol: Total RNA was isolated using the Agilent absolutely RNA miniprep kit. Samples were processed by mRNA enrichment and rRNA removal.

tag: strain

value: Brain, Amygdala

tag: developmental stage

value: Adult

value: female

value: No access to alcohol


title: SPL13D


title: Water drinking-2nd batch [Water4]


title: SPL13A


title: Water drinking-2nd batch [Water5]


title: 28KI

value: Left Kidney


title: Water drinking-2nd batch [Water3]


title: SPL12B


title: Water drinking-2nd batch [Water2]


title: 33LG


title: 30KI


title: Water drinking-2nd batch [Water1]


title: Chronic alcohol drinking-2nd batch [Chronic6]

value: Every-other-day access to 20% alcohol for a month


title: SPL11A


title: 27KI


title: 26KI


title: Chronic alcohol drinking-2nd batch [Chronic4]


title: 24RV

value: Right Ventricle


title: SPL9D


title: SPL11B


title: Acute alcohol drinking-2nd batch [Acute5]

value: Single access to 20% alcohol


title: 25KI


title: Chronic alcohol drinking-2nd batch [Chronic1]


title: Chronic alcohol drinking-2nd batch [Chronic5]


title: 23RV


title: Chronic alcohol drinking-2nd batch [Chronic3]


title: Acute alcohol drinking-2nd batch [Acute4]


title: Acute alcohol drinking-2nd batch [Acute3]


title: Acute alcohol drinking-2nd batch [Acute2]


title: 22RV


title: Acute alcohol drinking-2nd batch [Acute1]


title: 29KI


title: SPL9A_rep2


title: SPL9A_rep1


title: 21RV


title: Water drinking-1st batch [43]


title: SPL8D1


title: Water drinking-1st batch [42]


title: Chronic alcohol drinking-2nd batch [Chronic2]


title: Water drinking-1st batch [41]


title: SPL9B


title: Water drinking-1st batch [40]


title: 18RA

value: Right Atrium


title: Acute alcohol drinking-1st batch [35]


title: SPL8A_rep2

value: leaves


title: SPL8A_rep1


title: 17RA


title: Acute alcohol drinking-1st batch [34]


title: Acute alcohol drinking-1st batch [36]


title: SPL7B


title: 16RA


title: SPL7D


title: 15RA


title: Acute alcohol drinking-1st batch [33]


title: SPL7A


title: VOF F0 sperm-1

first: Wen-Long

last: Zhao

address: Guangyuan road 145#

institute: The International Peace Maternity and Child Health Hospital

data_processing:
We applied quality and adapter trimming to FastQ files with the Perl Programm Trim Galore (version 0.4.3).
Bismark v0.16.3 mapping to reference genome
methylKit Differential methylation analysis was performed using methylKit (Version 1.4.0)
Genome_build: mm10_GRCm38
Supplementary_files_format_and_content: TXT file contain differential methylation results

source_name: VOF F0 sperm-1

extract_protocol:
The cauda epididymis was removed and sperm swam out in Tyrode's solution at 37℃ in a humidified 5% CO2 atmosphere for 15 min.And genomic sperm DNA was extracted using the Easy Pure Genomic DNA Kit (EE101, Transgen Biotech, Beijing, China).
phenol-chloroform extraction followed by bisulfite treatment,converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013

value: sperm

value: 18 month old


title: VOF F0 sperm-2

source_name: VOF F0 sperm-2


title: 14RA


title: YF F0 sperm-3

source_name: YF F0 sperm-3

value: 2 month old


title: 20RV

value: WT control mouse


title: SPL8B


title: YF F0 sperm-2

source_name: YF F0 sperm-2


title: 19RV

value: musENH5 KO mouse

value: musENH5 Knockout, 16.5 hours hypobaric hypoxia, 8% O2


title: Chronic alcohol drinking-1st batch [39]


title: SPL6D

value: Magne-HALO Tag beads (Promega, G7282)


title: YF F0 sperm-1

source_name: YF F0 sperm-1


title: Chronic alcohol drinking-1st batch [37]

value: Brain, Amygdala


title: SPL6B


title: Chronic alcohol drinking-1st batch [38]

value: Adult


title: SPL6A_rep2


title: 11LV

value: Left Ventricle


title: SPL6A_rep1


title: 12LV

value: WT control mouse, 16.5 hours hypobaric hypoxia, 8% O2