description:
4967_21_KEP_Treg_Lymph_nodes_-_12_7_18_CGTACGT_S39
70K Tregs isolated from KEP lymph nodes (n = 1)

source_name: KEP TDLN Treg

value: 225mm2 spontaneous mammary KEP tumor

value: Lymph node (CD3+CD4+CD25+)


status: Public on Mar 01 2022

type: SRA

city: AMSTERDAM

first: Kevin

last: Kos

email: k.kos@nki.nl, k.d.visser@nki.nl

state: NOORD-HOLLAND

address: PLESMANLAAN 121

department: Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description:
4967_28_KEP_Treg_blood_-_18_5_18_TGACCAA_S43
70K Tregs isolated from KEP blood (n = 1)

library_source: transcriptomic

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script that gives the same output as HTSeq-count.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample; differential expression results

molecule: total RNA

organism: Mus musculus

source_name: KEP blood Treg

growth_protocol: Single cells suspensions were prepared from the WT and K14cre;Cdh1F/F;Trp53F/F mice bearing 225mm2  mammary tumors from blood, spleen, lungs, TDLNs, tumor and healthy mammary gland. Tumors were subjected to digestion for 1h, 37 degrees: 3mg/mL Collagenase A (Roche) in serum free DMEM (Dulbecco), Deoxyribonuclease I from bovine  pancreas (DNAse) 25μg/mL (Sigma-Aldrich). Lungs were enzymatically digested in 100 µg/mL Liberase Tm (Roche) under continuous rotation for 30 minutes at 37 °C. Erilysis was performed for lungs/blood

extract_protocol:
Tregs were flow cytometrically sorted in RLT buffer (qiagen) +1% b-mercapto-ethanol for the subsequent extraction of total RNA using RNAeasy mini kit (Qiagen). Total RNA was extracted using according to the manufacturer’s protocol.
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0 as assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared using standard Illumina protocols, analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

treatment_protocol: single cells were stained with fluorescencently conjugated monoclonal atibodies against CD3, CD4, CD25,CD45, CD8 and live/dead marker to identify their cell surface expression. Tregs were identified as live, CD45+, CD3+, CD4+, CD8-, CD25+

tag: strain background

value: FVB/N

tag: genotype

tag: tumor stage

tag: tissue

value: blood (CD3+CD4+CD25+)


description:
4967_25_KEP_Treg_tumor_-_18_5_18_ATCACGA_S42
30K Tregs isolated from KEP tumor (n = 1)

source_name: KEP Tumor Treg

value: Tumor (CD3+CD4+CD25+)


description:
4967_27_KEP_Treg_tumor_-_12_7_18_TTAGGCA_S34
70K Tregs isolated from KEP tumor (n = 1)


description:
4967_18_KEP_Treg_spleen_-_12_7_18_GTGAAAC_S33
70K Tregs isolated from KEP spleen (n =1)

source_name: KEP Spleen Treg

value: Spleen (CD3+CD4+CD25+)


description:
4967_23_KEP_Treg_lungs_-_22_6_18_ACTGATA_S38
30K Tregs isolated from KEP lungs (n = 1)

source_name: KEP lung Treg

value: Lungs (CD3+CD4+CD25+)


description:
4967_24_KEP_Treg_lungs_-_12_7_18_ATTCCTT_S41
49K Tregs isolated from KEP lungs (n = 1)


description:
4967_11_WT_Treg_mammary_gland_-_8_5_18_GGCTACA_S26
30K Tregs isolated from WT mammary gland (n = 3)

source_name: WT MG Treg

value: WT

value: mammary gland(CD3+CD4+CD25+)


description:
4967_20_KEP_Treg_Lymph_nodes_-_22_6_18_GTTTCGG_S35
70K Tregs isolated from KEP lymph nodes (n = 1)


description:
4967_29_KEP_Treg_blood_-_22_6_18_ACAGTGA_S37
17K Tregs isolated from KEP blood (n = 1)


description:
4967_19_KEP_Treg_Lymph_nodes_-_18_5_18_GTGGCCT_S36
70K Tregs isolated from KEP lymph nodes (n = 1)


title: 4967_9_WT_Treg_lungs_-_4_6_18_GATCAGA

description:
4967_9_WT_Treg_lungs_-_4_6_18_GATCAGA_S15
35K Tregs isolated from WT lungs (n = 3)

source_name: WT lungs Treg


title: 4967_8_WT_Treg_lungs_-_8_5_18_ACTTGAA

description:
4967_8_WT_Treg_lungs_-_8_5_18_ACTTGAA_S25
70K Tregs isolated from WT lungs (n = 3)


description:
4967_26_KEP_Treg_tumor_-_22_6_18_CGATGTA_S32
70K Tregs isolated from KEP tumor (n = 1)


title: 4967_7_WT_Treg_lungs_-_2_5_18_CAGATCA

description:
4967_7_WT_Treg_lungs_-_2_5_18_CAGATCA_S24
53K Tregs isolated from WT lungs (n = 3)


description:
4967_6_WT_Treg_Lymph_nodes_-_4_6_18_GCCAATA_S21
62K Tregs isolated from WT lymph nodes (n = 3)

source_name: WT LN Treg


description:
4967_5_WT_Treg_Lymph_nodes_-_8_5_18_ACAGTGA_S23
70K Tregs isolated from WT lymph nodes (n = 3)


description:
4967_30_KEP_Treg_blood_-_12_7_18_GCCAATA_S44
70K Tregs isolated from KEP blood (n = 1)


description:
4967_12_WT_Treg_mammary_gland_-_4_6_18_CTTGTAA_S20
9K Tregs isolated from WT mammary gland (n = 3)


description:
4967_17_KEP_Treg_spleen_-_22_6_18_GTCCGCA_S31
70K Tregs isolated from KEP spleen (n =1)


title: 4967_14_WT_Treg_blood_-_8_5_18_AGTTCCG

description:
4967_14_WT_Treg_blood_-_8_5_18_AGTTCCG_S28
9K Tregs isolated from WT blood (n = 3)

source_name: WT blood Treg


description:
4967_16_KEP_Treg_spleen_-_18_5_18_CCGTCCC_S30
70K Tregs isolated from KEP spleen (n =1)


description:
4967_10_WT_Treg_mammary_gland_-_2_5_18_TAGCTTA_S17
9K Tregs isolated from WT mammary gland (n = 3)


title: SUM159PT_Par_Input

city: Seoul

first: Kyung-min

last: Lee

address: 222 Wangsimni-ro

country: South Korea

institute: Hanyang University

library_source: genomic

data_processing:
raw fastq files were trimmed by TrimGalore and then aligned to human reference genome (hg38) using BWA
Low quality reads and duplicate reads were removed from aligned files using Sambamba and Samtools
Model-based Analysis of ChIPSeq (MACS) software tool (v.2.1.2) was used to call peaks
All peaks were annotated using ChipSeeker and differential binding activity was calculated using DiffBind
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
DNA was purified using QIAquick PCR Purification Kit
Libraries from 5–10 ng ChIP DNA were prepared using KAPA Hyper Library Preparation Kit

tag: cell line background

tag: cell type

value: parental cells


title: SUM159PT_Tax-R_1 [S7]

description:
processed data file:
159_TaxR_NormalizedCount.txt

data_processing:
In the raw fastq files, the ends of sequences with remaining adapter or quality scores <25 were trimmed. Any sequence less than 35bp was removed.
The trimmed fastq files were aligned to the selected reference genome using HiSAT2.
After marking duplicates using SAMBAMBA, genes, transcripts and exons were counted using featureCounts and StringTie.
DESeq2 package was used for analysis of differentially expressed genes and normalization of counts.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: NormalizedCount

extract_protocol:
RNA were extracted using Maxwell® RSC simplyRNA Cells Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: treatment


description:
4967_22_KEP_Treg_lungs_-_18_5_18_GAGTGGA_S40
70K Tregs isolated from KEP lungs (n = 1)


title: SUM159PT_Tax-R_2 [S8]


title: 4967_15_WT_Treg_blood_-_4_6_18_ATGTCAG

description:
4967_15_WT_Treg_blood_-_4_6_18_ATGTCAG_S29
20K Tregs isolated from WT blood (n = 3)


title: 4967_3_WT_Treg_spleen_4_6_18_TTAGGCA

description:
4967_3_WT_Treg_spleen_4_6_18_TTAGGCA_S18
70K Tregs isolated from WT spleen (n = 3)

source_name: WT Spleen Treg


title: MDA-MB-436_Tax-R_2 [S4]

description:
processed data file:
436_TaxR_NormalizedCount.txt


title: SUM159PT_Par_1 [S5]


title: SUM159PT_Tax-R_Input

value: Taxol-resistant cells


title: 4967_1_WT_Treg_spleen_-_2_5_18_ATCACGA

description:
4967_1_WT_Treg_spleen_-_2_5_18_ATCACGA_S16
70K Tregs isolated from WT spleen (n = 3)


title: MDA-MB-436_Par_2 [S2]


title: SUM159PT_Tax-R_MYC_ChIP

tag: chip antibody

value: Myc (Santa Cruz Biotechnology, Cat# sc-40X, Lot# A3120)


title: SUM159PT_Par_MYC_ChIP


description:
4967_4_WT_Treg_Lymph_nodes_-_2_5_18_TGACCAA_S22
70K Tregs isolated from WT lymph nodes (n = 3)


title: DSP-1001250003218-C-C12

city: Seattle

first: Stephanie

last: Zimmerman

state: WA

address: 530 Fairview Ave N

country: USA

institute: NanoString Technologies

data_processing:
Library strategy: GeoMx Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Human_11CPA_RawCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, probe information, and raw probe count matrix for each probe and sample
Supplementary_files_format_and_content: Human_11CPA_CollapsedTargetCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, processing information, and target-level count matrix for each gene target and sample
Supplementary_files_format_and_content: Human_11CPA_SampleAnnotations: xlsx file containing sample annotations

source_name: FFPE Human Cell Pellet Array

extract_protocol:
Samples were incubated with the human Whole Transcriptome Atlas RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: panel

value: WTA

tag: scan

value: GLASS

tag: plate

tag: roilabel


title: SUM159PT_Par_2 [S6]


title: DSP-1001250003218-C-C08


title: DSP-1001250003218-C-C10


title: DSP-1001250003218-C-C06


title: MDA-MB-436_Tax-R_1 [S3]


title: DSP-1001250003218-C-C11


title: DSP-1001250003218-C-C05

value: HEL


title: DSP-1001250003218-C-C04


title: MDA-MB-436_Par_1 [S1]


title: DSP-1001250003218-C-C09


title: DSP-1001250003218-C-C03


title: Mouse Brain Cortex - FMRP_KO_Rep3

city: Lyon

first: Kiran

last: Padmanabhan

address: 32-34 avenue Tony Garnier

department: IGFL

country: France

institute: ENS-Lyon

data_processing:
Base calling performed using Guppy (v4.0.11)
Mapping to the reference mouse transcriptome mm10 (Ensembl) using Minimap2 (v2.17) with the following flags “-ax map-ont -N 100” and only primary alignments were kept
Sorting and indexing of reads were performed using Samtools (v1.9)
Poly(A) length estimation was performed using Nanopolish (v0.13.2) with the default setting and transcripts with less than 10 reads per condition were filtered out. t-tests were used on average poly(A) length in each sample to identify statistically significant genotype-dependent poly(A) length changes
Isoform quantification was performed using Salmon (v1.5.2) in alignment-based mode and differential isoform expression was performed using DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: Excel file

source_name: Mouse Brain Cortex

extract_protocol:
brain cortex was extracted and poly(A) RNA was isolated using µMACS mRNA Isolation kit (130-075-101)
Five hundred ng of RNA was used for library preparation for direct RNA sequencing with SQK-RNA002 kit (Oxford Nanopore). Sequencing was performed using PromethION with the FLO_PRO002 flow cell (Oxford Nanopore)

value: Brain Cortex

tag: strain

tag: phenotype

value: Fmr1 KO

tag: sequencing

value: Direct RNA sequencing - Oxford Nanopore PromethION


title: DSP-1001250003218-C-B11


title: DSP-1001250003218-C-C01


title: Mouse Brain Cortex - FMRP_KO_Rep1


title: DSP-1001250003218-C-C07


title: 4967_2_WT_Treg_spleen_-_8_5_18_CGATGTA

description:
4967_2_WT_Treg_spleen_-_8_5_18_CGATGTA_S19
70K Tregs isolated from WT spleen (n = 3)


title: 4967_13_WT_Treg_blood_-_2_5_18_AGTCAAC

description:
4967_13_WT_Treg_blood_-_2_5_18_AGTCAAC_S27
30K Tregs isolated from WT blood (n = 3)


title: DSP-1001250003218-C-B10


title: DSP-1001250003218-C-C02

value: DAUDI


title: Mouse Brain Cortex - FMRP_KO_Rep2


title: Mouse Brain Cortex - WT_Rep1

value: Wild Type


title: DSP-1001250003218-C-B12


title: DSP-1001250003218-C-B06


title: DSP-1001250003218-C-B05


title: DSP-1001250003218-C-B08


title: DSP-1001250003218-C-B04


title: Mouse Brain Cortex - WT_Rep2


title: WT-N3752_Hi-C_double-digest_DpnII+MseI

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

data_processing:
All in situ Hi-C contact maps and other analyses presented in this manuscript were generated using the program suite HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/index.html) (Ramírez et al. 2018), using version 3.5 for all analyses, except the program hicFindEnrichedContacts (version 2.2.3) for observed vs. expected matrix generation. Briefly, raw fastq files were mapped to the Neurospora genome (either version 12 or version 14 [this work]) using bowtie2 (version 2.3), with the --local and --reorder flags, and the Hi-C contact matrix was built with hicBuildMatrix using the default settings (with both DpnII [GATC] and MseI [TTAA] restriction sites used for quality control); resulting images of the contact matrix images were made with hicPlotMatrix. Contact map images are either presented as raw or Knight-Ruiz corrected (Knight and Ruiz 2012), performed with the hicCorrectMatrix program, to account for differences in restriction enzyme site distribution or sequencing bias of underlying DNA. Observed vs. expected plots were generated with hicFindEnrichedContacts, available under hicExplorer version 2.2; observed vs. expected matrices were also Knight-Ruiz corrected.
Since Hi-C replicate datasets showed local reproducibility (Figure S4), fastq files of DpnII or MseI replicates were merged into a single fastq file, which was used to create the contact matrix. The final dataset resulted in a merged DpnII dataset with 269.9M reads (89.0M valid reads) and a merged MseI dataset with 93.8M reads (20.4M valid reads). To generate a comprehensive dataset representative of the chromatin composition of the WT Neurospora genome from individual DpnII (euchromatic-specific; GATC recognition sequence) and MseI (heterochromatic-specific; TTAA recognition sequence) datasets, we calculated the percent of the Neurospora genome covered by H3K9me3 demarcating constitutive heterochromatin, which have an increased number of MseI sites due to the AT-rich nature of the underlying DNA. To this end, we generated bed files of a previously published H3K9me3 merged dataset (Jamieson et al. 2016; Klocko et al. 2019), subtracted the end point from the starting point to calculate the number of basepairs covered by H3K9me3 at each region, summed the total number of bases, and divided the H3K9me3-covered bases by the genome size to get the percentage (15.76%) of the Neurospora genome covered by H3K9me3. The comprehensive in situ Hi-C dataset was built by combining all replicate fastq files into a single fastq file containing appropriate numbers of valid MseI or DpnII PE100 reads that, when combined, would provide 15.76% MseI-derived contacts and 84.24% DpnII-derived contacts. In this case, 21.4M reads (3.8M valid reads) were removed from MseI replicate #4, and the resulting MseI matrix using 72.4M reads (16.7M valid reads) was combined to the complete DpnII matrix (270M reads, 89.2M valid reads); this fastq file was used to build the comprehensive matrix, which contains 342.2M reads (105.9M valid reads) and was subject for all further analysis.
Genome_build: GSE71024_neurospora_crassa_or74a_12_genome_FIXED.fasta (version 12; Galazka et al., 2016, Genome Research) or nc14_genome-seq-name.fasta (version 14; this work)
Supplementary_files_format_and_content: the .h5 files are contact matrices generated by hicExplorer; briefly, this 3D matrix is divided into bins, and the interactions between the bins is reported - either raw contact counts, Knight-Ruiz corrected contact counts, or the calculated ratio of observed vs. expected contact numbers on a log10 scale (the observed vs. expected contact matrix was also subject to Knight-Ruiz correction).

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: To grow WT Neurospora culture, 25 mL cultures containing 1x Vogel’s medium + 1.5% sucrose were inoculated with 1.25x10^8 conidia, (harvested from ~six baby slants by vortexing with water; conidia were washed twice prior to use) and grown at 32 °C with shaking at 200 revolutions per minute (RPM) for ~four hours until ~90% of conidia had germinated, and growth tubes were ~4x the length of the initial conidia.

extract_protocol:
First, the concentration of genomic DNA per spheroplast aliquot was determined by resuspending one aliquot per culture replicate in 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM sodium ethylenediaminetetraacetic acid [Na EDTA], 0.5% [w/v] sodium dodecyl sulfate [SDS]) plus 100 mg proteinase K (Invitrogen) and incubated at 65°C for 16 hours. The volume was then increased to a total of 500 μL using TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA), and 40 mg RNase A (Invitrogen) was added. Aliquots were incubated at 37 °C for 30 min, and genomic DNA was extracted with twice 25:24:1 phenol:chloroform:isoamyl alcohol (25:24:1; ThermoFisher cat# AC327115000), once with chloroform, and precipitated with 0.1 volume sodium acetate (pH 5.2) and 1 volume isopropanol, centrifuged (10 minutes, 13k rpm), and the resulting DNA pellet was washed once with 70% (v/v) ethanol, dried for 10 min in a Savant SpeedVac (ThermoFisher, Model # DNA120-115), and resuspended in 50 μL TE. The total DNA concentration per pellet was determined by quantifying 2 μL of the total resuspension of genomic DNA (50 μL) using a Qubit 3.0 HS DNA quantification kit (ThermoFisher cat# Q33217). Spheroplasts containing 3.5 μg of genomic DNA were resuspended in 270 μL of 1x restriction enzyme buffer (either DpnII, above) and 50 μL hydrated glass beads were added (Sigma-Aldrich #G1145, Acid washed, 150-212 μm). Spheroplasts were lysed by vortexing tubes for 30 seconds followed by 30 seconds on ice; five total cycles were performed. Following the settling of the beads, 270 μL of supernatant (and cell debris, if possible) were moved to a new tube. SDS was added to 0.625% final concentration (30 μL of 6.25% stock), tubes incubated at 62 °C for 7 minutes, and immediately placed on ice. Triton X-100 was added to a final concentration of 1% [33 μL of 10% (v/v)] and 10x DpnII or MseI buffer was added to account for added volumes of SDS, Triton and enzymes. Genomic DNA in chromatin was then digested with 200 U DpnII and MseI (double digest) for 16 hours at 37°C while nutating. Samples were then centrifuged for 3000 rpm for 10 minutes, the supernatant was removed, and the pellets, which contained permeabilized nuclei and chromatin, were resuspended in 83 μL of 1x DpnII buffer. Sticky ends were blunted in a 100 μL reaction with 30 μM each of dCTP, dGTP, dTTP, Biotin-14-dATP (Invitrogen cat# 19524-016), and 25 U of Klenow (large fragment). Reactions were mixed by pipetting and incubated at 37°C for 60 minutes with nutating. An additional 110 μL of 1x DpnII or MseI buffer was added to the samples (210 μL total chromatin volume), and ligation reactions with 1x T4 Ligation buffer, 1% Triton X-100, 100 μg/mL BSA, and 1675 U of T4 DNA ligase were immediately prepared and incubated at 16 °C for 4 hours. Proteinase K (250 μg total; Gold Biotechnology cat# 97062-238) was added and reactions were decrosslinked at 65°C once overnight (~16 hours) and following the addition of another 250 μg of proteinase K, reactions were decrosslinked a second time for 2 hours. Cooled samples were extracted twice with phenol:chloroform:isoamyl alcohol, the aqueous fraction was transferred to a 2.0 mL microcentrifuge tube, and the volume increased to 500 μL with additional TE buffer. Ligated DNA circles were precipitated by addition of 0.1x volume 3M sodium acetate pH 6.0, 2.5x volumes 100% ethanol, 40 μg glycogen (ThermoFisher cat# R0561), incubation at -80 °C for 30 minutes followed by centrifugation at 13,000 rpm for 15 minutes. Pellets were washed once with 70% ethanol, dried at RT for 10 minutes in a speedvac, and resuspended in 50 μL TE. RNaseA (20 μg; SigmaAldrich cat# R4875) was added and samples were incubated at 37 °C for 30 minutes. An additional 450 μL TE was added, and ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform. The aqueous fraction was transferred to a new 2.0 mL microcentrifuge tube, and ligation products were precipitated (0.1x 3M sodium acetate pH 6.0 and 2.5x 100% ethanol were added, and tubes were incubated at -80 °C for 20 minutes and centrifuged at 13,000 rpm for 10 minutes), washed, dried, resuspended in 25 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA) and stored at -20 °C. To remove biotin-dATP from unligated DNA ends, 50 μL reactions consisting of 1x NEB buffer 2.1, 100 μM each of dATP and dGTP, and 5 U of T4 DNA polymerase were incubated at 12 °C for 2 hours and quenched with EDTA (final concentration 10 mM), and the reaction volume was increased to 500 μL with TE/10. DNA ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform, transferred to a 2.0 mL microcentrifuge tube, and ethanol precipitated (0.1x volume 3M sodium acetate, pH 6.0 and 2.5x volume 100% ethanol were added, tubes were incubated at -80 °C for 20 minutes, centrifuged at 13,000 rpm for 10 minutes, washed, dried, and DNA pellets were resuspended in 500 μL TE/10). Ligation products were sheared by sonication (Qsonica, Model Q55; amplitude = 30%, 30 seconds sonication, 30 second incubation on ice between pulses). Sheared, biotinylated ligation products were captured on streptavidin magnetic beads (Dynabeads M280, Invitrogen cat# 11205D) equilibrated with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) at RT for 30 minutes, with pipetting every 10 minutes. Beads were washed on a magnetic rack three times with 1x BW buffer, twice with TE/10, and resuspended in 25 uL TE/10 buffer.
Hi-C libraries for Illumina sequencing were prepared using a NEBNext Ultra II kit (New England Biolabs cat# E7645) with corresponding Multiplex Barcode sets (NEB cat# E7335 and E7500) according to the manufacturer’s protocol, with the following exceptions, as all steps were performed using the Hi-C library attached to the magnetic streptavidin beads: following the adapter ligation and USER enzyme digestion, magnetic beads were washed five times with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) and once with TE/10, and resuspended in 15 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA); PCR enrichment of the barcoded Hi-C library off streptavidin beads used either eight or 15 cycles (or an initial fifteen PCR cycles, whereupon the beads were washed three times with TE/10, and were re-amplified by an additional 8 cycles, for a total of 23 cycles) and following the separation of the aqueous PCR product from the magnetic beads, the PCR product was cleaned with a 1:1 ratio of Ampure XP beads (Agencourt, Beckman-Coulter) per the manufacturer’s protocol, resuspended in 25 μL TE/10, and quantified by a Qubit HS reaction. Prior to sequencing, all libraries were assessed for quality via Fragment Analyzer and qPCR (Genomics and Cell Characterization Core Facility [GC3F], University of Oregon). Indexed in situ Hi-C libraries were pooled and sequenced on an Illumina HiSeq 4000 or an Illumina NovaSeq 6000 at the Genomics and Cell Characterization Core Facility [GC3F] at the University of Oregon as 100 nucleotide (nt) paired-end (PE100) sequencing runs. Hi-C dataset fastq files are provided in table S1.

treatment_protocol: Methanol-free formaldehyde was added to a final concentration of 1% and cultures were incubated 10 minutes at room temperature (RT; ~25°C) with shaking at 100 RPM for crosslinking; 1 M Tris-HCl [pH 8 at 25°C] (Hoffman et al. 2015) was added to a final concentration of 125 mM and cultures were incubated at RT for 10 minutes, shaking at 100 RPM, to quench the reaction. Conidia were harvested by centrifugation (4000 RPM, 3 min) and resuspended gently in 20 mL spheroplasting buffer (1 M sorbitol, 100 mM KPO4 [pH 7.5]) with b-mercaptoethanol added to 30mM. Conidia were pelleted again and resuspended in 20 mL spheroplasting buffer with b-mercaptoethanol added to 1mM. VinoTaste (Novozymes; powder dissolved in water to a stock solution of 50 mg/mL) was added to 50mg and strains were digested at 30°C, shaking at 100 RPM, for 60 min. Spheroplasts were harvested by centrifugation (3500 RPM, 2 min) and pellets were washed twice with 20 mL Spheroplasting buffer, followed by three washes of the buffer of the 1x restriction enzyme to be used for digestion, here DpnII buffer (100 mM NaCl, 50 mM Tris-HCl [pH 7.9 at 25°C], 10 mM MgCl2, 100 μg/mL BSA). Washed pellets were resuspended in 3.5 mL of the same restriction enzyme buffer, split into four – 1 mL aliquots in 1.7 mL Eppendorf tubes, pelleted (10,000 rpm, 5 min), whereupon the supernatant was removed, and spheroplast pellets were stored at -80°C.

tag: developmental stage

value: asexual, unsynchronized cells


title: DSP-1001250003218-C-B07


title: Mouse Brain Cortex - WT_Rep3


title: DSP-1001250003218-C-B02


title: DSP-1001250003218-C-B03


title: DSP-1001250003218-C-B01


title: DSP-1001250003218-C-A12


title: DSP-1001250003218-C-A06


title: DSP-1001250003218-C-A10


title: Biopsy_DCD_EVLP_563

type: RNA

city: Toronto

first: Mingyao

last: Liu

state: ON

address: 101 College Street

department: Latner Thoracic Resaerch Laboratories

country: Canada

institute: University Health Network

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing:
Affymetrix CEL files were imported and processed using RMA in R version 3.5.0 with the affy package. We used an alternative CDF probset description file from Brainarray at the University of Michigan (Nucleic Acid Research 33 (20), e175; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp): clariomdhumanhsentrezgcdf_22.0.0.zip
clariomdhumanhsentrezgcdf_22.0.0.zip

label: biotin

source_name: Biopsy, donor type: DCD

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

tag: donor type

value: DCD

tag: evlp type

value: EVLP


title: DSP-1001250003218-C-A03


title: DSP-1001250003218-C-B09


title: DSP-1001250003218-C-A07


title: DSP-1001250003218-C-A11


title: Biopsy_DBD_Non-EVLP_552

source_name: Biopsy, donor type: DBD

value: DBD

value: Non-EVLP


title: Biopsy_DCD_EVLP_565


title: Biopsy_DBD_Non-EVLP_560


title: Biopsy_DCD_Non-EVLP_544


title: DSP-1001250003218-C-A05


title: Biopsy_DBD_Non-EVLP_569


title: Biopsy_DBD_Non-EVLP_549


title: Biopsy_DBD_Non-EVLP_562


title: Biopsy_DBD_Non-EVLP_535


title: Biopsy_DBD_Non-EVLP_561


title: Biopsy_DBD_Non-EVLP_545


title: Biopsy_DBD_Non-EVLP_551


title: DSP-1001250003218-C-A04


title: DSP-1001250003218-C-A01

value: NTC


title: DSP-1001250003218-C-A09


title: DSP-1001250003218-C-A08


title: HC2

city: DALLAS

last: Yan

state: TEXAS

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Raw sequencing data was processed by Genomics Sequencing & Microarray Core at UT Southwestern Medical Center. Primary data analysis was done using CLC-Biosystems Genomic Workbench analysis programs to generate quantitative data, including Reads Per Kilobase of transcript per Million mapped reads (RPKM) values.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM of each transcript

source_name: PBMCs

extract_protocol:
RNeasy Mini Kit (QIAGEN, 74104)
mRNAseq-Strand specific Library were prepared for sequencing

tag: disease state

value: healthy patient

value: PBMCs


title: Biopsy_DCD_EVLP_538


title: SKI

value: THES patient

tag: tissue


title: TLCN242

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description:
Hepatocellular carcinoma
TLCN242

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCh38) by STAR (v2.6.1a) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts.

source_name: Hepatocellular carcinoma

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen,  Hilden, Germany).
Libraries were constructed using Illumina TruSeq RNA Access Library Prep kit according to the manufacturers

tag: etiology

value: NBNC

tag: ctnnb1 status

value: mut

tag: efs days

tag: efs event

tag: os days

tag: os event


title: DSP-1001250003218-C-A02

tag: panel

value: WTA

tag: scan


title: Biopsy_DBD_Non-EVLP_529


title: TLCN269

description:
Hepatocellular carcinoma
TLCN269

value: wt


title: TLCN240

description:
Hepatocellular carcinoma
TLCN240


title: TLCN249

description:
Hepatocellular carcinoma
TLCN249


title: TLCN264

description:
Hepatocellular carcinoma
TLCN264


title: Biopsy_DCD_EVLP_521


title: TLCN250

description:
Hepatocellular carcinoma
TLCN250


title: Biopsy_DCD_EVLP_518


title: TLCN267

description:
Hepatocellular carcinoma
TLCN267


title: Biopsy_DBD_Non-EVLP_523


title: Biopsy_DBD_Non-EVLP_508


title: TLCN283

description:
Hepatocellular carcinoma
TLCN283


title: Biopsy_DCD_EVLP_526


title: Biopsy_DCD_EVLP_496


title: Biopsy_DBD_Non-EVLP_520


title: Biopsy_DBD_Non-EVLP_498


title: TLCN235

description:
Hepatocellular carcinoma
TLCN235


title: TLCN236

description:
Hepatocellular carcinoma
TLCN236


title: Biopsy_DBD_Non-EVLP_505


title: Biopsy_DCD_EVLP_490


title: Biopsy_DCD_Non-EVLP_517


title: Biopsy_DCD_Non-EVLP_499


title: Biopsy_DBD_Non-EVLP_530


title: TLCN231

description:
Hepatocellular carcinoma
TLCN231


title: TLCN230

description:
Hepatocellular carcinoma
TLCN230


title: TLCN229

description:
Hepatocellular carcinoma
TLCN229


title: Biopsy_DCD_EVLP_503


title: Biopsy_DCD_EVLP_486


title: Biopsy_DBD_Non-EVLP_495


title: TLCN211

description:
Hepatocellular carcinoma
TLCN211


title: TLCN209

description:
Hepatocellular carcinoma
TLCN209


title: TLCN207

description:
Hepatocellular carcinoma
TLCN207


title: Biopsy_DBD_EVLP_488


title: TLCN201

description:
Hepatocellular carcinoma
TLCN201


title: Biopsy_DCD_EVLP_484


title: Biopsy_DBD_Non-EVLP_482


title: TLCN192

description:
Hepatocellular carcinoma
TLCN192

value: HCV


title: TLCN202

description:
Hepatocellular carcinoma
TLCN202


title: TLCN135

description:
Hepatocellular carcinoma
TLCN135


title: Biopsy_DCD_Non-EVLP_483


title: Biopsy_DBD_Non-EVLP_481


title: Biopsy_DCD_EVLP_477


title: Biopsy_DCD_EVLP_471


title: Biopsy_DBD_Non-EVLP_475


title: TLCN053

description:
Hepatocellular carcinoma
TLCN053

value: HBV


title: HC1


title: TLCN104

description:
Hepatocellular carcinoma
TLCN104


title: TLCN222

description:
Hepatocellular carcinoma
TLCN222


title: TLCN027

description:
Hepatocellular carcinoma
TLCN027


title: Biopsy_DBD_Non-EVLP_468


title: Biopsy_DBD_EVLP_464


title: Biopsy_DBD_Non-EVLP_462


title: TLCN024

description:
Hepatocellular carcinoma
TLCN024


title: Biopsy_DBD_EVLP_457


title: TLCN598

description:
Hepatocellular carcinoma
TLCN598


title: TLCN588

description:
Hepatocellular carcinoma
TLCN588


title: TLCN585

description:
Hepatocellular carcinoma
TLCN585


title: TLCN586

description:
Hepatocellular carcinoma
TLCN586


title: TLCN583

description:
Hepatocellular carcinoma
TLCN583


title: TLCN567

description:
Hepatocellular carcinoma
TLCN567


title: TLCN532

description:
Hepatocellular carcinoma
TLCN532


title: TLCN499

description:
Hepatocellular carcinoma
TLCN499


title: TLCN493

description:
Hepatocellular carcinoma
TLCN493


title: TLCN014

description:
Hepatocellular carcinoma
TLCN014


title: TLCN481

description:
Hepatocellular carcinoma
TLCN481


title: TLCN474

description:
Hepatocellular carcinoma
TLCN474


title: Biopsy_DBD_Non-EVLP_476


title: Biopsy_DBD_Non-EVLP_450


title: Biopsy_DCD_Non-EVLP_435


title: Biopsy_DBD_Non-EVLP_456


title: Biopsy_DCD_EVLP_428


title: Biopsy_DCD_Non-EVLP_444


title: Biopsy_DBD_Non-EVLP_443


title: Biopsy_DCD_Non-EVLP_431


title: Biopsy_DCD_EVLP_426


title: Biopsy_DBD_Non-EVLP_467


title: Biopsy_DBD_Non-EVLP_422


title: Biopsy_DCD_EVLP_415


title: Biopsy_DBD_EVLP_423


title: TLCN450

description:
Hepatocellular carcinoma
TLCN450


title: Biopsy_DBD_Non-EVLP_407


title: TLCN431

description:
Hepatocellular carcinoma
TLCN431


title: TLCN427

description:
Hepatocellular carcinoma
TLCN427


title: TLCN426

description:
Hepatocellular carcinoma
TLCN426


title: Biopsy_DCD_Non-EVLP_430


title: Biopsy_DCD_EVLP_433


title: TLCN491

description:
Hepatocellular carcinoma
TLCN491


title: Biopsy_DCD_EVLP_399


title: Biopsy_DBD_Non-EVLP_404


title: Biopsy_DCD_EVLP_401


title: TLCN473

description:
Hepatocellular carcinoma
TLCN473


title: TLCN422

description:
Hepatocellular carcinoma
TLCN422


title: TLCN409

description:
Hepatocellular carcinoma
TLCN409


title: Biopsy_DCD_EVLP_384


title: TLCN400

description:
Hepatocellular carcinoma
TLCN400


title: TLCN404

description:
Hepatocellular carcinoma
TLCN404


title: TLCN399

description:
Hepatocellular carcinoma
TLCN399


title: Biopsy_DCD_EVLP_375


title: Biopsy_DCD_EVLP_390


title: Biopsy_DBD_Non-EVLP_414


title: TLCN398

description:
Hepatocellular carcinoma
TLCN398


title: Biopsy_DBD_Non-EVLP_380


title: TLCN349

description:
Hepatocellular carcinoma
TLCN349


title: TLCN318

description:
Hepatocellular carcinoma
TLCN318


title: TLCN345

description:
Hepatocellular carcinoma
TLCN345


title: Biopsy_DBD_EVLP_373


title: Biopsy_DCD_Non-EVLP_367


title: Biopsy_DBD_Non-EVLP_350


title: Biopsy_DCD_Non-EVLP_368


title: TLCN292

description:
Hepatocellular carcinoma
TLCN292


title: TLCN397

description:
Hepatocellular carcinoma
TLCN397


title: TLCN371

description:
Hepatocellular carcinoma
TLCN371


title: Biopsy_DCD_EVLP_344


title: TLCN584

description: Hepatocellular carcinoma

extract_protocol:
Total RNA was extracted from frozen snaps using an AllPrep DNA/RNA mini kit (Qiagen,  Hilden, Germany).
Libraries were constructed using Illumina TruSeq Stranded mRNA kit according to the manufacturers


title: TLCN580

description: Hepatocellular carcinoma


title: TLCN587

description: Hepatocellular carcinoma


title: TLCN597

description: Hepatocellular carcinoma


title: Biopsy_DCD_Non-EVLP_335


title: Biopsy_DBD_Non-EVLP_338


title: TLCN308

description:
Hepatocellular carcinoma
TLCN308


title: Biopsy_DCD_EVLP_339


title: Biopsy_DCD_EVLP_330


title: TLCN579

description: Hepatocellular carcinoma


title: Biopsy_DCD_Non-EVLP_321


title: Biopsy_DBD_Non-EVLP_319


title: TLCN344

description:
Hepatocellular carcinoma
TLCN344


title: Biopsy_DCD_EVLP_328


title: TLCN556

description: Hepatocellular carcinoma


title: Biopsy_DCD_Non-EVLP_315


title: TLCN562

description: Hepatocellular carcinoma


title: TLCN554

description: Hepatocellular carcinoma


title: TLCN550

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_381


title: TLCN548

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_304


title: Biopsy_DCD_Non-EVLP_300


title: Biopsy_DBD_Non-EVLP_308


title: TLCN540

description: Hepatocellular carcinoma


title: TLCN545

description: Hepatocellular carcinoma


title: Biopsy_DCD_Non-EVLP_293


title: Biopsy_DBD_Non-EVLP_297


title: TLCN543

description: Hepatocellular carcinoma


title: Biopsy_DCD_Non-EVLP_299


title: TLCN537

description: Hepatocellular carcinoma


title: TLCN533

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_290


title: Biopsy_DBD_Non-EVLP_281


title: Biopsy_DCD_EVLP_288


title: TLCN565

description: Hepatocellular carcinoma


title: Biopsy_DCD_Non-EVLP_355


title: Biopsy_DBD_Non-EVLP_284


title: TLCN527

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_285


title: TLCN516

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_265


title: TLCN510

description: Hepatocellular carcinoma


title: TLCN517

description: Hepatocellular carcinoma


title: TLCN514

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_249


title: TLCN509

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_252


title: Biopsy_DCD_EVLP_268


title: TLCN526

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_248


title: Biopsy_DCD_EVLP_272


title: Biopsy_DBD_Non-EVLP_239


title: TLCN504

description: Hepatocellular carcinoma


title: TLCN487

description: Hepatocellular carcinoma


title: TLCN503

description: Hepatocellular carcinoma


title: TLCN500

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_240


title: Biopsy_DBD_Non-EVLP_235


title: Biopsy_DCD_EVLP_236


title: TLCN478

description: Hepatocellular carcinoma


title: TLCN485

description: Hepatocellular carcinoma


title: TLCN471

description: Hepatocellular carcinoma


title: TLCN395

description:
Hepatocellular carcinoma
TLCN395


title: TLCN476

description: Hepatocellular carcinoma


title: TLCN469

description: Hepatocellular carcinoma


title: TLCN483

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_227


title: TLCN468

description: Hepatocellular carcinoma


title: TLCN467

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_230


title: TLCN465

description: Hepatocellular carcinoma


title: TLCN464

description: Hepatocellular carcinoma


title: TLCN451

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_212


title: Biopsy_DCD_Non-EVLP_222


title: Biopsy_DCD_Non-EVLP_215


title: Biopsy_DBD_Non-EVLP_207


title: Biopsy_DCD_Non-EVLP_234


title: TLCN442

description: Hepatocellular carcinoma


title: Biopsy_DCD_EVLP_208


title: Biopsy_DBD_Non-EVLP_206


title: Biopsy_DCD_EVLP_194


title: Biopsy_DCD_EVLP_200


title: Biopsy_DCD_EVLP_225


title: Biopsy_DCD_EVLP_190


title: NW2

type: genomic

city: Beijing

first: Changyi

last: Xie

address: Qinghua yuan street

department: School of Environment

country: China

institute: Tsinghua University

description: GeoChip data for soil sample collected at nitrogen addition, warming, replicate 2

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: uncultured soil microorganism

source_name: Soil microbes in mangrove sediments

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Genomic DNA was extracted from 5 g of sediment sample by a freeze-grinding procedure (Zhou et al 1996). To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

treatment_protocol: On 9th July, 2015, soil samples were collected from all of the plots. Two independent sedimental soil cores at a depth of 0-20 cm in each plot were collected using hand-held PVC corers and mixed thoroughly  to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory. Soil samples were preserved at -80°C before DNA extraction.

tag: treatment

value: nitrogen addition, warming


title: NW4

description: GeoChip data for soil sample collected at nitrogen addition, warming, replicate 4


title: Biopsy_DBD_Non-EVLP_192


title: NW3

description: GeoChip data for soil sample collected at nitrogen addition, warming, replicate 3


title: N2

description: GeoChip data for soil sample collected at nitrogen addition, no warming, replicate 2

value: nitrogen addition, no warming


title: Biopsy_DCD_Non-EVLP_189


title: N3

description: GeoChip data for soil sample collected at nitrogen addition, no warming, replicate 3


title: N4

description: GeoChip data for soil sample collected at nitrogen addition, no warming, replicate 4


title: N1

description: GeoChip data for soil sample collected at nitrogen addition, no warming, replicate 1


title: NW1

description: GeoChip data for soil sample collected at nitrogen addition, warming, replicate 1


title: TLCN440

description: Hepatocellular carcinoma


title: TLCN438

description: Hepatocellular carcinoma


title: TLCN441

description: Hepatocellular carcinoma


title: W3

description: GeoChip data for soil sample collected at no nitrogen addition, warming, replicate 3

value: no nitrogen addition, warming


title: W4

description: GeoChip data for soil sample collected at no nitrogen addition, warming, replicate 4


title: TLCN436

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_188


title: TLCN432

description: Hepatocellular carcinoma


title: superKH_B2_2_NF

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

data_processing:
Nanopore data processing: MinKNOW software (20.06.5). The raw data were acquired as fast5 files, and base-called with Guppy basecaller software (v4.2.2). Low quality and short reads (Phred score < 7 and length < 1,000 bp, respectively) were removed using NanoFilt (version 2.7.1). To detect the integration sites of the transfected plasmid, we performed the following three steps: i) to extract the reads containing a sequence/sequences of the exogenous DNA material, BLASTn (2.10.1+) search was carried out, using the exogenous sequence as the query against the database containing sequencing reads that passed the quality filters (E-value < 1.0E-30, -outfmt 6); ii) 500 bases of upstream and downstream found in the step i reads containing endogenous DNAs were extracted with SeqKit (version 0.13.2) and the following parameters: grep -nrp, subseq -r; iii) the integration sites in the ge-nome were found with BLASTn search of upstream and downstream regions (see the step ii) against the Pv11 genome (Genbank Assembly Accession Id GCA_018290105.1, E-value < 1.0E-30, -outfmt 6, max_target_seq 1, max_hsps 1). The results were visual-ized with the DensityMap tool.
ATAC-seq data processing: Illumina Casava software used for basecalling. Reads trimmed with NGmerge, version 0.3. Next, survived reads were aligned to Pv11_5.2 genome assembly with bowtie2 --very-sensitive -k 10 (bowtie2 version 2.3.4.3). Aligned sam files were sorted, converted to BAM format, and indexed with samtools v1.11-5. Duplicated reads were removed with picard MarkDuplicates script (v 1.115). Finnaly, clusters were defined by Genrich v0.6.
Genome_build: Pv11_5.2
Supplementary_files_format_and_content: Genrich peaks for ATAC-seq experiments. The txt file includes coordinates, AUC information, p.values, and summits positions.

organism: Polypedilum vanderplanki

growth_protocol: Cells were grown as described previously. For the culture, IPL-41 medium (Thermo Fisher Scientific, Waltham, MA) supplemented with 2.6 g/L tryptose phosphate broth (Becton, Dickinson and Company, Franklin Lakes, NJ), 10% (v/v) fetal bovine serum, and 0.05% (v/v) of an antibiotic and antimycotic mixture (peni-cillin, amphotericin B, and streptomycin; Sigma Aldrich, St. Louis, MO) was used, and the medium is designated hereafter as complete IPL-41 medium.

extract_protocol:
For ATAC-seq, 75,000 cells were centrifuged at 500 g for 5 minutes at 4°С, and washed once with cold PBS and 600 mM trehalose solution for normal condition and trehalose-treated samples, respectively. The cells were resuspended in lysis buffer for 10 minutes. Nextera DNA Sample Prep Kit (Illumina) was used for the following tagmentation reaction, and the products were purified with MinElute PCR Purification Kit (Qiagen). For MinION sequencing, high molecular wight DNAs were extracted with NucleoBond HMW DNA Kit (TaKaRa Bio, Shiga, Japan). The DNA solution was further subjected to Short Read Elim-inator Kit (NIPPON Genetics.co., Ltd, Tokyo, Japan) in order to deplete short DNA frag-ments.
Oxford Nanopore MinION platform with a Flow Cell R9.4.1. Illumina HiSeq2500 ATAC-seq PE libraries.
genomic Nanopore and ATAC-seq

treatment_protocol: Cells were incubated in preconditioning medium (600 mM trehalose containing 10% (v/v) complete IPL-41 medium) for 48 h at 25°C.

value: normal culture condition

tag: cell type

value: B2  subcloned from the KH cell pool


title: T3

value: 48 h-trehalose treatment


title: W1

description: GeoChip data for soil sample collected at no nitrogen addition, warming, replicate 1


title: T2


title: T1


title: Biopsy_DBD_EVLP_184

value: DBD

value: EVLP


title: Biopsy_DCD_Non-EVLP_365

value: DCD

value: Non-EVLP


title: Biopsy_DBD_Non-EVLP_179


title: Biopsy_DBD_Non-EVLP_183


title: CK4

description: GeoChip data for soil sample collected at no nitrogen addition, no warming, replicate 4

value: no nitrogen addition, no warming


title: CK3

description: GeoChip data for soil sample collected at no nitrogen addition, no warming, replicate 3


title: Super_KH_4C

value: 4C subcloned from the KH cell pool


title: CK1

description: GeoChip data for soil sample collected at no nitrogen addition, no warming, replicate 1


title: K1

value: before trehalose treatment


title: TLCN429

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_177


title: W2

description: GeoChip data for soil sample collected at no nitrogen addition, warming, replicate 2


title: K3


title: Biopsy_DBD_Non-EVLP_172


title: K2


title: TLCN425

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_174


title: TLCN418

description: Hepatocellular carcinoma


title: TLCN420

description: Hepatocellular carcinoma

value: mut


title: TLCN419

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_159


title: Biopsy_DBD_Non-EVLP_167


title: D^high 4h

city: Aarhus C

first: martin

middle: R

last: Jakobsen

address: Høegh-Guldbergs Gade 10, Bygn. 1115

department: Biomedicine

country: Denmark

institute: Aarhus University

description: Total RNA was purified from pDCs from a donor infected with SARS-CoV-2 after 4 hrs

hyb_protocol: 20h of probe hybridization was done according to the manufacturer’s instructions

scan_protocol: Nanostring nCounter® SPRINT Profiler was used to scan the probes

data_processing: Data analysis and normalization was done using Nanostring nSolver 4.0

source_name: HSPC-pDC

label_protocol: 30 ng RNA was loaded into nCounter PanCancer Immune Profiling Panel (cat# XT-CSO-HIP1-12) plus a custom made PanelPlus of the following genes: NFE2L2, TMEM173, MB21D1, IFNLR1, irf9, IFNL3, IFNL4, AIM2, TREX1, ENPP1, PCBP1, PQBP1, G3BP1, STIM1, LRRC8A, SLC19A1, NLRC3, NLRX1, ZDHHC1, TRIM56, TRIM32, RNF5, ULK1, TTLL4, TTLL6, AGBL5, AGBL4, PRKDC, DDX41

growth_protocol: Human CD34+ Hematopoietic Stem and Progenitor Cells (HSPC), obtained from cord blood, were differentiated into HSPC-pDC using SFEM II medium supplemented with 20 U/mL penicillin and 20 μg/mL streptomycin, 100 ng/mL Flt3-L, 50 ng/mL TPO, 100 ng/mL SCF, 20 ng/mL IL-3 and 1 µM SR1. After a 21-day differentiation period, the HSPC-pDC were enriched by negative magnetic selection and primed in RPMI-1640 medium supplemented with 10% (v/v) heat-inactivated fetal calf serum, 2 mM L-glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin, 250 U/mL IFNβ, 12.5 ng/mL IFNγ and 20 ng/mL IL-3.

extract_protocol: total RNA was purified from cells using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: HSPC-pDCs from two donors were exposed to SARS-CoV-2 at 1 MOI (for 4, 24 or 48 hrs and mock treated samples at 4 and 48 hrs), after which cell pellets were collected and RNA extracted with the RNeasy mini kit (Qiagen).

tag: source cell type

value: hematopoietic stem and progenitor cells

tag: derived cell type

value: pDC

value: exposed to SARS-CoV-2

tag: time after exposure


title: D^low 24h

description: Total RNA was purified from pDCs from a donor infected with SARS-CoV-2 after 24 hrs


title: D^low 4h


title: D^high 48h

description: Total RNA was purified from pDCs from a donor infected with SARS-CoV-2 after 48 hrs


title: D^high 24h


title: TLCN421

description: Hepatocellular carcinoma

value: HCV

value: wt


title: TLCN415

description: Hepatocellular carcinoma


title: D^low 48h


title: drim2.4_8_17h

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

data_processing:
Illumina HiSeq v4
Reads were filtered using trimmomatic and mapped on the Aspergillus nidulans genome assembly (A_nidulans_FGSC_A4_version_s10-m03-r07). Mapping was performed using BWA  and reverse transcripts were counted using python script HTSeq and exons as annotation features.
Normalization and statistics were done using R/Bioconductor and the limma and edgeR packages, using mean-variance weighting (voom) and TMM normalisation
Genome_build: A_nidulans_FGSC_A4_version_s10-m03-r07
Supplementary_files_format_and_content: Matrix table with RPKM values for each experiment
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Aspergillus nidulans

source_name: Fungal cultures

growth_protocol: A spore density of 4*106 spores/mL was inoculated in either 60 mL or 200 mL of liquid AMM in 300 mL or 1000 mL Erlenmeyer flasks, respectively, and the culture grown at 37 °C and 180 rpm. The time of cultivation was 48 hours for secondary metabolism conditions, 17 hours for primary metabolism conditions or 40 hours for the onset of secondary metabolism. AMM was prepared containing Aspergillus salt stock solution, modified Hutner’s TE solution, 50 mM glucose and 10 mM nitrate.

extract_protocol: poly A enrichment, NEXTERA library prep kit

treatment_protocol: Fungal cultures were grown in duplicates for 17 hours to analyze primary metabolism and 48 hours (A1153 and OE) or 54 hours (rimOΔ) to analyze secondary metabolism. The knockout strain has a lower glucose uptake rate, so we decided to choose to harvest the cultures 8 hours after glucose was depleted from the medium.

tag: genotype

tag: time point

tag: replicate

value: Replicate 2


title: drim2.4_7_17h

value: Replicate 1


title: Biopsy_DBD_Non-EVLP_161

tag: donor type

tag: evlp type


title: Oegr_3_5_17h


title: Oegr_3_4_17h


title: Oegr_3_9_48h


title: TLCN410

description: Hepatocellular carcinoma

tag: etiology

tag: ctnnb1 status


title: drim2.4_13_54h


title: Biopsy_DBD_Non-EVLP_157


title: A1153_4b_48h

value: WildType


title: Oegr_3_10_48h


title: A1153_2_17h


title: TLCN408

description: Hepatocellular carcinoma

tag: efs days

tag: efs event


title: Placenta

city: Beltsville

first: George

middle: E.

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

data_processing:
Programs FastQC (0.11.5) and Trim Galore (0.4.5) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus ARS-UCD1.2) using bowtie2 under the Bismark software (0.19.0)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position,strand, coverage for methylated cytosine, coverage for unmethylated cytosine, CG type, three bases near the cytosine.

organism: Bos taurus

source_name: Placenta

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from somatic tissues and sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.

tag: breed

value: Holstein

tag: tissue

value: Placenta


title: Biopsy_DBD_Non-EVLP_154

value: DBD


title: Biopsy_DBD_Non-EVLP_155


title: TLCN407

description: Hepatocellular carcinoma

tag: os days

tag: os event


title: TLCN373

description: Hepatocellular carcinoma

value: HBV


title: Biopsy_DBD_Non-EVLP_149

value: Non-EVLP


title: Biopsy_DBD_Non-EVLP_145


title: DtMusc

source_name: Skeletal Muscle

value: Hereford

value: Skeletal Muscle


title: A1153_5b_48h


title: TLCN374

description: Hepatocellular carcinoma


title: TLCN372

description: Hepatocellular carcinoma


title: Sperm_B03

source_name: Sperm

value: Sperm


title: CK2

description: GeoChip data for soil sample collected at no nitrogen addition, no warming, replicate 2

tag: treatment

value: no nitrogen addition, no warming


title: Biopsy_DBD_Non-EVLP_142


title: Sperm_A03


title: TLCN348

description: Hepatocellular carcinoma

value: mut


title: TLCN341

description: Hepatocellular carcinoma


title: DtRum

source_name: Rumen

value: Rumen


title: DoRum


title: TLCN396

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_141


title: Biopsy_DBD_Non-EVLP_135


title: Biopsy_DBD_Non-EVLP_133


title: Biopsy_DBD_Non-EVLP_140


title: TLCN307

description: Hepatocellular carcinoma


title: TLCN340

description: Hepatocellular carcinoma


title: TLCN301

description: Hepatocellular carcinoma


title: TLCN317

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_129


title: TLCN291

description: Hepatocellular carcinoma


title: TLCN281

description: Hepatocellular carcinoma

value: NBNC


title: TLCN289

description: Hepatocellular carcinoma


title: TLCN285

description: Hepatocellular carcinoma


title: TLCN280

description: Hepatocellular carcinoma


title: TLCN302

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_132


title: Biopsy_DBD_Non-EVLP_134


title: TLCN277

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_119


title: Biopsy_DBD_Non-EVLP_127


title: Biopsy_DBD_Non-EVLP_124


title: A1153_1_17h


title: Fibroblast_rep2_RNAseq

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
3'-Tag-RNA-seq: Unique molecular identifiers (UMIs), corresponding to the first six bases of every read, were appended to fastq headers using umi_tools (v1.0.0) extract (options –extract-method=string –bc-pattern=NNNNNN -L).
3'-Tag-RNA-seq: Prior to alignment, the ARS-UCD1.2 bovine genome assembly was indexed with the Ensembl genome annotation (v99) using STAR (v2.7.2a) with option –sjdbOverhang 100. Reads were then aligned to ARS-UCD1.2 using STAR (options –outFilterMultimapNmax 20 – alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverReadLmax 0.04 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –outSAMunmapped None –outFilterType BySJout –outFilterScoreMinOverLread 0.3 –outFilterMatchNminOverLread 0.3 –seedSearchStartLmax 30).
3'-Tag-RNA-seq: Duplicates and low quality (q<5) alignments were removed using umi_tools (v1.0.0) dedup and SAMtools  (v1.9), respectively.
3'-Tag-RNA-seq: Alignments were assigned to genes using HTSeq-count (v0.10.0) (options –mode=intersection-nonempty –stranded=yes) considering alignments overlapping with exons and 3’ untranslated regions (UTRs). Because 3’-Tag-RNA-Seq biases reads towards the 3’ UTR ends, which are not often accurately annotated in cattle, the 3’ ends of currently annotated genes (Ensembl v99) were extended by 1,000 bp. Ends were only extended into regions that were not previously annotated.
CUT&Tag: Raw sequencing reads were trimmed with trim_galore (v0.4.0) using options -q 20 -stringency 1 –paired –length 10.
CUT&Tag: Trimmed reads were  aligned to the ARS-UCD1.2 assembly with BWA mem (v0.7.17-r1188) with default settings.
CUT&Tag: Duplicates and low-quality alignments (q<3) were removed with Picard-tools (v2.8.1) and SAMtools (v1.7), respectively.
CUT&Tag: From filtered alignments, normalized genome-wide coverage was calculated by deepTools bamCoverage (v3.2.0) as counts per million in 50 bp windows.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Text files containing raw expression counts for genes in the Ensembl annotation (v101).
Supplementary_files_format_and_content: Bigwig files that contain normalized genome-wide coverage as counts per million in 50 bp windows.

source_name: Fibroblasts

growth_protocol: Derivation of bESC was carried out using day 7-8 zona-free single blastocysts. Unhatched SCNT, IVF and PAR blastocysts were treated with 10 mg/mL Pronase (10165921001, Roche) for zona pellucida degradation. Thereafter, whole blastocysts were individually plated in a 0.1% gelatin (G9391, Sigma) coated 48-well dish which contained a monolayer of mouse embryonic fibroblasts (MEF) (A34180, Gibco), and incubated in NBFR media supplemented with 10 μM Rho Kinase inhibitor Y-27632 (ROCKi) (ALX-270-333, Enzo) and 1% v/v Antibiotic/Antimycotic (20004, JR Scientific) at 37˚C, 5% CO2  (passage zero; P0). NBFR media consisted of a mixture of 1:1 DMEM/F12 medium (11320-033, Gibco) and Neurobasal medium (21103-049, Gibco), 0.5% v/v N-2 Supplement (17502-048, Gibco), 1% v/v B-27 Supplement (17504-044, Gibco), 2 mM MEM Non-essential Amino Acid Solution, 1% v/v GlutaMAX Supplement, 100 U/mL Penicillin and 100 μg/mL Streptomycin, 0.1 mM 2-mercaptoethanol (M6250, Sigma), 20 ng/mL human FGF2 (100-18B, PeproTech), 2.5 μM IWR-1 (I0161, Sigma) and 1% v/v low fatty acid Bovine Serum Albumin (BSA) (0219989950, MP Biomedicals). After 24 h, blastocysts that failed to adhere to the feeder layer were pressed against the bottom of the dish to promote attachment using a 22G needle and incubated for another 24 h. Blastocysts that still failed to adhere were discarded. After 48 h of plating, culture media was changed daily. Antibiotic/antimycotic supplementation was maintained during P0, whereas ROCKi supplementation was done every time cells were passed or cryopreserved. During the first three weeks of derivation, the whole culture was passed every seven days in a 1:1 split ratio using Tryple Express (12604013, Gibco) and re-seeded into fresh MEF. Between the third and fourth week of derivation (passage 3 or 4), bESC colonies appeared and the cell line was considered established. Cells that were not established after 5 weeks in culture were discarded. Once established, bESC were passed every 3-4 days in a 1:5 or 1:10 split ratio, depending on the cell line. Cells were checked for Mycoplasma sp. contamination once a month using LookOut® Mycoplasma PCR Detection Kit (MP0035, Sigma) following manufacturer’s instructions.

extract_protocol:
3'-Tag-RNA-seq: RNA was isolated from fibroblasts and bESC devoid of MEF using the RNeasy Mini Kit (74104, Qiagen) including DNase treatment with the RNase-Free DNase Set (79254, Quiagen) following manufacturer’s instructions. RNA was quantified using the Qubit RNA BR Assay Kit (Q10211, Invitrogen) and its integrity was studied by determining the RNA quality index (RQI) using a Bio-Rad Experion™ Automated Electrophoresis System.
3'-Tag-RNA-seq: Isolated RNA was submitted to DNA Technologies and Expression Analysis Core at the University of California Davis Genome Center for library preparation and sequencing. Sequencing was performed on the Illumina HiSeq 4000 platform and produced single-end 90 bp reads.
CUT&Tag was performed as previously described (Kaya-Okur et al., 2019). The protocol was adapted for 100,000 cells per sample. Briefly, cells were thawed as previously described, then washed and incubated with conditioned ConA bead slurry (10 µl per 100,000 cells) for 10 min at room temperature in an end-over-end rotator. Cells were then incubated overnight on a nutator at 4°C with a 1:50 dilution with primary antibody. Afterwards, cells were incubated with the secondary antibody guinea pig anti-rabbit IgG antibody (ABIN101961, AntibodiesOnline) in a 1:100 dilution for 1 h at room temperature using a nutator. Cells were then washed and mixed with the pA-Tn5 adapter complex in a 1:250 dilution for 1 h at room temperature in a nutator. Following incubation with the pA-Tn5 adapter complex, cells were washed and then incubated in tagmentation buffer for 1 h at 37°C.  After 1 h, tagmentation was stopped and DNA fragments were solubilized by adding 10 μL 0.5M EDTA, 3 μL 10% SDS and 2.5 μL 20 mg/mL Proteinase K to each sample, followed by full-speed vortexing and incubation for 1 h at 50°C. DNA fragments were extracted using phenol-cloroform-isopropide procedure and any remaining RNA was degraded by incubating the samples in a 1:400 RNAse A dilution for 10 min at 37°C. Finally, DNA fragments were amplified with the universal i5 primer, barcoded i7 primers, and NEBNext HiFi 2x PCR Master mix. PCR cycling was conducted as follows: 72°C for 5 min, 98°C for 30 sec, followed by 14 cycles of 98°C for 10 sec and 63°C for 10 sec, and a final extension step of 72°C for 1 min. PCR products were purified using Ampure XP beads. After equimolar pooling of barcoded libraries, samples were submitted to DNA Technologies and Expression Analysis Core, University of California Davis Genome Center, for bead clean-up to remove PCR primers and fragments longer than 1,000 bp. Sequencing was performed on the Illumina HiSeq 4000 platform and produced paired-end 40 bp reads.

tag: Sex

value: Male

tag: passage


title: Fibroblast_rep3_RNAseq

value: Female


title: Fibroblast_rep1_IgG

data_processing:
Library strategy: CUT&Tag
3'-Tag-RNA-seq: Unique molecular identifiers (UMIs), corresponding to the first six bases of every read, were appended to fastq headers using umi_tools (v1.0.0) extract (options –extract-method=string –bc-pattern=NNNNNN -L).
3'-Tag-RNA-seq: Prior to alignment, the ARS-UCD1.2 bovine genome assembly was indexed with the Ensembl genome annotation (v99) using STAR (v2.7.2a) with option –sjdbOverhang 100. Reads were then aligned to ARS-UCD1.2 using STAR (options –outFilterMultimapNmax 20 – alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverReadLmax 0.04 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –outSAMunmapped None –outFilterType BySJout –outFilterScoreMinOverLread 0.3 –outFilterMatchNminOverLread 0.3 –seedSearchStartLmax 30).
3'-Tag-RNA-seq: Duplicates and low quality (q<5) alignments were removed using umi_tools (v1.0.0) dedup and SAMtools  (v1.9), respectively.
3'-Tag-RNA-seq: Alignments were assigned to genes using HTSeq-count (v0.10.0) (options –mode=intersection-nonempty –stranded=yes) considering alignments overlapping with exons and 3’ untranslated regions (UTRs). Because 3’-Tag-RNA-Seq biases reads towards the 3’ UTR ends, which are not often accurately annotated in cattle, the 3’ ends of currently annotated genes (Ensembl v99) were extended by 1,000 bp. Ends were only extended into regions that were not previously annotated.
CUT&Tag: Raw sequencing reads were trimmed with trim_galore (v0.4.0) using options -q 20 -stringency 1 –paired –length 10.
CUT&Tag: Trimmed reads were  aligned to the ARS-UCD1.2 assembly with BWA mem (v0.7.17-r1188) with default settings.
CUT&Tag: Duplicates and low-quality alignments (q<3) were removed with Picard-tools (v2.8.1) and SAMtools (v1.7), respectively.
CUT&Tag: From filtered alignments, normalized genome-wide coverage was calculated by deepTools bamCoverage (v3.2.0) as counts per million in 50 bp windows.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Text files containing raw expression counts for genes in the Ensembl annotation (v101).
Supplementary_files_format_and_content: Bigwig files that contain normalized genome-wide coverage as counts per million in 50 bp windows.

tag: antibody

value: IgG, C15410206, Diagenode


title: TLCN274

description: Hepatocellular carcinoma


title: Fibroblast_rep1_H3K27me3

value: H3K27me3, C15410195, Diagenode


title: Biopsy_DBD_Non-EVLP_113


title: TLCN272

description: Hepatocellular carcinoma

value: wt


title: Fibroblast_rep1_H3K9me3

value: H3K9me3, C15410193, Diagenode


title: TLCN265

description: Hepatocellular carcinoma


title: Fibroblast_rep1_H3K4me3


title: bESC-PAR_rep1_RNAseq

source_name: Embryonic stem cells


title: bESC-SCNT_rep3_H3K27me3


title: Biopsy_DBD_Non-EVLP_114


title: Biopsy_DBD_Non-EVLP_123


title: Biopsy_DBD_Non-EVLP_111


title: Biopsy_DBD_Non-EVLP_112


title: Biopsy_DBD_Non-EVLP_109


title: Biopsy_DBD_Non-EVLP_108


title: Biopsy_DBD_Non-EVLP_107


title: bESC-SCNT_rep2_IgG


title: bESC-SCNT_rep3_H3K9me3


title: Fibroblast_rep1_RNAseq


title: bESC-SCNT_rep3_RNAseq


title: bESC-SCNT_rep3_H3K4me3


title: bESC-SCNT_rep2_H3K27me3


title: drim2.4_12_54h

tag: genotype

value: Replicate 1


title: TLCN252

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_100

value: DBD


title: TLCN244

description: Hepatocellular carcinoma


title: bESC-SCNT_rep2_RNAseq


title: TLCN262

description: Hepatocellular carcinoma


title: bESC-SCNT_rep2_H3K4me3


title: Biopsy_DBD_Non-EVLP_97


title: TLCN241

description: Hepatocellular carcinoma


title: TLCN255

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_103


title: TLCN238

description: Hepatocellular carcinoma


title: bESC-SCNT_rep1_H3K9me3


title: Biopsy_DBD_Non-EVLP_94


title: bESC-SCNT_rep1_H3K4me3


title: bESC-SCNT_rep1_RNAseq


title: bESC-SCNT_rep2_H3K9me3


title: bESC-IVF_rep3_IgG


title: Biopsy_DBD_Non-EVLP_87


title: TLCN227

description: Hepatocellular carcinoma


title: TLCN234

description: Hepatocellular carcinoma


title: bESC-SCNT_rep1_H3K27me3


title: TLCN223

description: Hepatocellular carcinoma


title: TLCN221

description: Hepatocellular carcinoma


title: bESC-IVF_rep2_H3K9me3


title: bESC-IVF_rep2_H3K27me3


title: bESC-IVF_rep2_H3K4me3


title: Biopsy_DBD_Non-EVLP_96


title: bESC-IVF_rep3_H3K9me3


title: TLCN203

description: Hepatocellular carcinoma


title: bESC-IVF_rep3_H3K27me3


title: Biopsy_DBD_Non-EVLP_147


title: bESC-IVF_rep2_RNAseq


title: bESC-IVF_rep3_H3K4me3


title: TLCN200

description: Hepatocellular carcinoma

value: HCV


title: bESC-IVF_rep1_RNAseq


title: bESC-IVF_rep3_RNAseq


title: bESC-IVF_rep1_H3K4me3


title: Biopsy_DBD_Non-EVLP_89

value: Non-EVLP


title: bESC-IVF_rep1_H3K27me3


title: TLCN199

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_85


title: DoMusc

value: Hereford


title: Biopsy_DBD_Non-EVLP_84


title: Neonatal_miRNA

city: shanghai

first: Yukang

last: Wu

address: siping road 1239

institute: tongji university

data_processing:
We use internal software SOAPnuke to filter reads, followed as:  1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 5%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format (see FASTQ Format in help page FASTQ Format).  Software information: SOAPnuke:  version：v1.5.2  parameters: -l 15 -q 0.2 -n 0.05  website: https://github.com/BGI-flexlab/SOAPnuke
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping  step. For HISAT which is much faster, sensitive and high accuracy analysis software.  Software information:  HISAT2:  Version: v2.0.4  Parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000  Website: http://www.ccb.jhu.edu/software/hisat
It is important to distinguish differential isoform relative abundance, from differential isoform  expression. Changes in relative abundance of isoforms, regardless of the expression change,  indicate a splicing-related mechanism. On the other hand, there can be measurable changes in the  expression of isoforms across samples, without necessarily changing the relative abundance, which  possibly indicates a transcription-related mechanism. We use rMATS] to detect differentially  splicing gene(that is differential isoform relative abundance between samples), a computational tool  to detect differential alternative splicing events from RNA-Seq data, it calculates the inclusion isoform  and skipping isofrom, shown as Figure6. The statistical model of MATS calculates the P-value and  false discovery rate ( FDR ) that the difference in the isoform ratio of a gene between two conditions,  in our project, gene that with FDR <= 0.05 is defined as significant differentially splicing gene ( DSG  ).  Software information:  rMATS:  Version: v3.2.5  Parameters: -analysis U -t paired -a 8  Website: http://rnaseq-mats.sourceforge.net
We mapped clean reads to reference using Bowtie2, and then calculate gene expression  level with RSEM . RSEM is a software package for estimating gene and isoform expression  levels from RNA-Seq data. Then, wecalculate pearson correlation between all samples using cor,  perform hierarchical clustering between all samples using hclust, and draw the diagrams with  ggplot2 with fuctions of R.  Software information:  Bowtie2 :  Version: v2.2.5  Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X  1000 --no-mixed --no-discordant -p 1 -k 200  Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml  RSEM :  Version: v1.2.12  Parameters: default  Website: http://deweylab.biostat.wisc.edu/ RSEM
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample ...

source_name: neonatal  heart tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

treatment_protocol: Heart were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.

tag: cell type

value: cardiomyocyte

tag: strain

tag: developmental stage

value: neonatal


title: Biopsy_DBD_Non-EVLP_83

tag: donor type

tag: evlp type


title: TLCN197

description: Hepatocellular carcinoma

tag: etiology

tag: ctnnb1 status


title: Biopsy_DBD_Non-EVLP_79


title: Biopsy_DBD_Non-EVLP_82


title: Biopsy_DBD_Non-EVLP_70


title: TLCN196

description: Hepatocellular carcinoma

tag: efs days

tag: efs event


title: E17_5

source_name: embryonic day 17.5 heart tissue

value: embryonic day 17.5


title: E14_5_miRNA

source_name: embryonic day 14.5 heart tissue

value: embryonic day 14.5


title: E14_5


title: E17_5_miRNA


title: Adult_miRNA

source_name: adult heart tissue

value: adult


title: Adult


title: bESC-IVF_rep1_H3K9me3

tag: replicate


title: TLCN186

description: Hepatocellular carcinoma

tag: os days


title: TLCN198

description: Hepatocellular carcinoma

tag: os event


title: E10_5_miRNA

source_name: embryonic day 10.5 heart tissue

value: embryonic day 10.5


title: E10_5


title: TLCN179

description: Hepatocellular carcinoma


title: TLCN180

description: Hepatocellular carcinoma


title: Neonatal


title: Biopsy_DBD_Non-EVLP_73

source_name: Biopsy, donor type: DBD


title: Biopsy_DBD_Non-EVLP_67


title: TLCN173

description: Hepatocellular carcinoma

value: mut


title: Esc_Atac_Stage29_2

city: Vienna

first: Hannah

last: Schmidbaur

address: Althanstraße 14, UZA1

department: Department of Neuroscience and Developmental Biology

institute: University of Vienna

description: Atac-seq

data_processing:
ATAC-seq: Quality of reads was assessed with fastqc. Trimming of reads was done with bbduk (ktrim=r qtrim=15 k=21 mink=8 hdist=0) from the bbtools package, Version 38.56. Reads were mapped to the E. scolopes chromosomal assembly (Lachesis) using Bowtie2 (--very-sensitive, -k 10, -p8). Peaks were called on aligned bam files with Genrich (-j -y -r -v).
Genome_build: Lachesis assembly from this study (a new assembly based on reads from GCA_004765925.1 but scaffolded with the hi-c data in GSM4770325.).
Supplementary_files_format_and_content: Narrow peak files (Genrich output)

organism: Euprymna scolopes

source_name: Pooled tissue of 3 whole embryos

extract_protocol: ATAC-seq library preparation was based on the OMNI-ATAC-seq method with modifications as described below. After removing the chorion and yolk sac, the embryos from stage 20, 24/25 and 28/29 were dissociated by Liberase treatment in PBS (1:100 dilution Unit of Liberase™, for 15 min at RT). Each library was obtained from 3 animals and 1.5 to 2 x104 K cells were used.  After cell dissociation, the dissociated squid cell suspensions were spun down (380 x g for 5 min at 4°C) and re-suspend in 750 μl of ice-cold lysis buffer no.1 by gentle pipetting. Then cells were again spun down (380 x g for 5 min at 4°C) and pellets were resuspended in 100 μl of ice-cold lysis lysis buffer no.2 and incubated on ice 5 min. Ice cold lysis buffer no. 3 (750 μl) was added on top of cell mixture and mixed gently. Immediately, cells were spun down (380 x g for 5 min at 4°C). The cell pellets were resuspended with 50 μl of Tn5 Transposase reaction mixture (Transposase reaction: 5 μl of the 5x Transposase buffer (in-home): 50 mM TAPS-NaOH (pH 8.5), 25 mM MgCl2, 50% DMF, 16.5 μl of PBS, 1 μl of 10% Tween-20 (0.1 % f. c.), 1 μl of 1% Digitonin (0.01 % f. c.), 5 μl of assembled in-home Tn5 (0.5 μg of assembled Tn5 was used for a reaction). Tn5 assembly with adapters was carried out following3. Transposition with Tn5 was carried out at 37°C for 1 hr with occasional agitation. The reaction was stopped by adding 5X the volume of PB buffer (QIAGEN) and vortexing for 30 second. Tn5 treated DNA was purified (QIAGEN mini purification kit) and eluted into 20 μl of EB buffer. Purified DNA solution (10 μl) was used for library amplification, and final amplification cycles were defined with intermediate qPCR.36,34. Final libraries were amplified with NEBNext® High-Fidelity 2X PCR Master Mix (NEB)). After PCR amplification, the libraries were purified with DNA purification beads. Sequencing was performed by 125 bp paired‐end mode at VBCF NGS.

value: E. scolopes, late stage emrbyo, stage 28/29

tag: tissue

value: Whole embryos, chorion and yolk removed

value: WT

value: Biological replicate 2


title: Esc_Atac_Stage20_2

description: Atac-seq

value: E. scolopes, early embryo, stage 20


title: TLCN163

description: Hepatocellular carcinoma

source_name: Hepatocellular carcinoma


title: Esc_Atac_Stage29_1

description: Atac-seq

value: Biological replicate 1


title: Esc_Atac_Stage25_2

description: Atac-seq

value: E. scolopes, middle stage embryo, stage 24/25


title: TLCN165

description: Hepatocellular carcinoma

value: HCV


title: Esc_Atac_Stage25_1

description: Atac-seq


title: Biopsy_DBD_Non-EVLP_69

value: DBD

value: Non-EVLP


title: Esc_Atac_Stage20_1

description: Atac-seq


title: Esc_Hic_Stage27

description: Hi-C data, restriction enzyme HindIII

data_processing:
HiC data: Alignment against unmasked reference genome were done with HicPro which uses Bowtie2 Version 7.3.1  with the following parameters; Global options: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder.  Chromosome scaffolding in Lachesis with the settings: RE_SITE_SEQ =AAGCTT, CLUSTER_CONTIGS_WITH_CENS = -1, CLUSTER_MIN_RE_SITES = 25, CLUSTER_MAX_LINK_DENSITY = 2, CLUSTER_NONINFORMATIVE_RATIO = 3, CLUSTER_DRAW_HEATMAP = 0, CLUSTER_DRAW_DOTPLOT = 1, ORDER_MIN_N_RES_IN_TRUNK = 15, ORDER_MIN_N_RES_IN_SHREDS = 15, Cluster_N = 46 Local options= --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder. Other settings: normalization maxiter = 100 filterlowcountpercent = 0.02 filterhighcountpercent = 0 EPS = 0.1. Chromosome scaffolding in Lachesis with the settings: RE_SITE_SEQ =AAGCTT, CLUSTER_CONTIGS_WITH_CENS = -1, CLUSTER_MIN_RE_SITES = 25, CLUSTER_MAX_LINK_DENSITY = 2, CLUSTER_NONINFORMATIVE_RATIO = 3, CLUSTER_DRAW_HEATMAP = 0, CLUSTER_DRAW_DOTPLOT = 1, ORDER_MIN_N_RES_IN_TRUNK = 15, ORDER_MIN_N_RES_IN_SHREDS = 15, Cluster_N = 46. Re-alignment of raw Hi-C reads to new Lachesis assembly was done with the same settings as described before.
Genome_build: GCA_004765925.1, Lachesis assembly from this study
Supplementary_files_format_and_content: Iced normalized Hi-C contact matrices
Sample1_20000_iced.matrix: Hicpro iced Hi-C contact matrix, binsize 20000bp
Sample1_40000_iced.matrix: Hicpro iced Hi-C contact matrix, binsize 40000bp
Sample1_100000_iced.matrix: Hicpro iced Hi-C contact matrix, binsize 100000bp

source_name: Pooled tissue of 30 whole embryos, stage 27 (staging after Lee et al. 2009)

extract_protocol: Hi-C protocol (see also supplementary note): After removing the chorion and yolk sac, embryos of stage ~27 were dissociated in Liberase in PBS (1:100 dilution Unit of Liberase ™, for 15 min at RT). The cells were collected by centrifugation (380 x g for 10 min at 4°C), and resuspended into 9 ml of 10 % FBS/PBS. The cells were fixed with formaldehyde (1 % f. c. (Merck (Burlington, Massachusetts, United States))) for 10 minutes at room temperature. Fixation was stopped by adding ice‐cold glycine (125 mM f. c. (Sigma-Andrich (St. Louis, Missouri, United States))). Fixed cells were collected by centrifugation (380 x g for 10 min at 4°C), and washed with ice-cold PBS twice (380 x g for 10 min at 4°C). Cells at a concentration of 1 × 106 per ml were collected and incubated in ice‐cold lysis buffer on ice (10 mM Tris–HCl pH 8, 10 mM NaCl, 0.2% Igepal CA‐630, 1 % Triton-X100, protease inhibitor cocktail EDTA free). After centrifugation to pellet the cell nuclei (380 x g for 10 min at 4°C) were washed once with 1.25x NEBuffer2 (New England Biolabs (Ipswich, Massachusetts, United States)). The nuclei were resuspended in 1.25x NEBuffer2. SDS (0.6 % f. c.) was added, and the mixture was incubated with agitation (950 rpm for 2 h at 37°C). Triton X‐100 (3.3 % f. c.) was added to quench the SDS, and the nuclei were incubated with agitation (950 rpm for 2 h at 37°C).   Restriction digestion with HindIII (from NEB; 2,000 U per 0.25 million cells) was performed overnight with agitation (950 rpm at 37°C). After chromatin digestion, the restriction sites were filled with biotin‐14‐dATP (Thermo Fisher (Waltham, Massachusetts, United States)), dCTP, dGTP, and dTTP, with Klenow (50 U per 0.5 million cells) for 1 h at 37°C with repeated agitation (700 rpm 10 sec and rest 30 sec for 1 h in a thermal cycler).   Ligation was performed overnight at 18°C (2000 U of T4 DNA ligase). After ligation, crosslinking was reversed by proteinase K treatment overnight at 65°C. An additional proteinase K incubation at 65°C for 2 h was followed with RNase A treatment and two sequential phenol/chloroform extractions. After DNA precipitation, the DNA was spun down (centrifugation with max-speed for 30 min at 4°C). The pellets were resuspended in 20 μl TE and the DNA concentration was determined using Qubit 2 device (Thermo Fisher).   20 μg of Biotinylated DNA was used for the library preparation. The biotin from non‐ligated fragment ends was removed with T4 DNA polymerase (NEB) for 30 min at 37°C and EDTA was added to stop the reaction (10 mM f. c.). DNA was sonicated using the Covaris system to generate DNA fragments with a size peak around 400 bp (Covaris S2 settings: duty factor: 10%; peak incident power: 5; time: 60 sec). After end repair with T4 DNA polymerase, Klenow Large fragment and T4 DNA polynucleotide kinase in the presence of dNTPs in T4 DNA ligation buffer (for 30 min at room temperature), the DNA was purified (QIAGEN mini purification kit (QIAGEN ( Hilden, Germany))).   A double‐size selection using DNA purification beads was performed and the size selected DNA was eluted in Elution buffer (QIAGEN). Biotinylated ligation products were isolated using pre-washed MyOne Streptavidin C1 Dynabeads (Life Technologies) on a magnet stand in binding buffer (5 mM Tris pH8, 0.5 mM EDTA, 1 M NaCl) for 30 min at room temperature. dA-tailing was carried on beads: dATP was added with Klenow exo‐ (for 1h at 3°C, NEB), then the enzyme was heat‐inactivated (20 min at 65°C). After two washes in binding buffer and one wash in T4 DNA ligation buffer, Illumina adapters were ligated onto Hi‐C ligation products bound to streptavidin beads in T4 DNA ligase by slow rotation (for 2 h at room temperature). After washing twice with wash buffer (5 mM Tris pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05 % Tween‐20) and then once with binding buffer, the DNA‐bound beads were resuspended in a final volume of 20 μl 1x NEBBuffer2. Captured biotinylated Hi‐C DNA was amplified by 9 cycles PCR amplification (with NEBNext® High-Fidelity 2X PCR Master Mix (NEB)). After PCR amplification, the Hi‐C libraries were purified with DNA purification beads. Hi‐C libraries were sequenced by paired‐end 50 bp mode at VBCF NGS facility (Vienna BioCenter, Vienna, Austria).

value: E. scolopes late emrbyo, stage 27

value: Biological replicate 1. One library was run in two lanes.


title: Biopsy_DBD_Non-EVLP_66


title: TLCN160

description: Hepatocellular carcinoma


title: TLCN175

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_65


title: Biopsy_DBD_Non-EVLP_56


title: Biopsy_DBD_Non-EVLP_61


title: Biopsy_DBD_Non-EVLP_63


title: TLCN156

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_48


title: Biopsy_DBD_Non-EVLP_52


title: Biopsy_DBD_Non-EVLP_36


title: MCF10.AT1 -Replicate 1

city: Houston

first: Anjana

last: Bhardwaj

state: Texas

address: 1515 Holcombe Blvd

department: Breast Surgical Oncology

institute: UT MD Anderson cancer Center

hyb_protocol: not provided

scan_protocol: not provided

data_processing: To identify the signatures of acquired resistance to fluvastatin, the total cellular RNA from 3 replicates of MCF10.AT1 and MCF10.AT1-R cells were subjected to Clariom D RNA profiling (ThermoFisher).  The raw signal intensity data in the CEL files was preprocessed and normalized by RMA (Robust Multichip Average) method using Bioconductor packages “affy” and “oligo”.  After preprocessing, we performed data quality assessment. The data was cleaned by removing the low expression and invariant genes.

source_name: MCF10.AT1 cells untreated, biological repl 1

label_protocol: not provided

growth_protocol: Cells were grown in MCF10.AT1 media

extract_protocol: Trizol

treatment_protocol: Cells were grown in MCF10.AT1 media with Fluvastatin treatment added in increamental doses from 1uM, 5uM, up to 20uM

tag: cell line

value: breast cancer

tag: sensitivity to fluvastatin

value: Fluvastatin sensitive


title: Biopsy_DBD_Non-EVLP_44


title: TLCN155

description: Hepatocellular carcinoma


title: MCF10.AT1-R -Replicate 1 (FVA resistant)

source_name: MCF10.AT1 -Resistant cells , biological repl 1

value: Fluvastatin resistant


title: TLCN153

description: Hepatocellular carcinoma


title: MCF10.AT1-R -Replicate 3 (FVA resistant)

source_name: MCF10.AT1 -Resistant cells , biological repl 3


title: MCF10.AT1-R -Replicate 2 (FVA resistant)

source_name: MCF10.AT1 -Resistant cells , biological repl 2


title: Biopsy_DBD_Non-EVLP_53


title: TLCN149

description: Hepatocellular carcinoma

value: wt


title: MCF10.AT1 -Replicate 3

source_name: MCF10.AT1 cells untreated, biological repl 3


title: MCF10.AT1 -Replicate 2

source_name: MCF10.AT1 cells untreated, biological repl 2


title: TLCN152

description: Hepatocellular carcinoma

value: mut


title: TLCN143

description: Hepatocellular carcinoma


title: TLCN144

description: Hepatocellular carcinoma


title: TLCN145

description: Hepatocellular carcinoma


title: TLCN142

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_34


title: Biopsy_DBD_Non-EVLP_33


title: Biopsy_DBD_Non-EVLP_30


title: Biopsy_DBD_Non-EVLP_29


title: Biopsy_DBD_Non-EVLP_15


title: Biopsy_DBD_Non-EVLP_14


title: Biopsy_DBD_Non-EVLP_16


title: Biopsy_DBD_Non-EVLP_35


title: Biopsy_DBD_Non-EVLP_28


title: M_1

city: beijing

first: liang

middle: sheng

last: xian

address: shuangqing road

institute: chinese academy of science

data_processing:
Reads were filtered and then mapped to the reference genome sequence (UCSC hg38) with HISAT
Sequences were aligned to reference genes with Bowtie2 tool
The gene expression level was determined by the RSEM software
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Fastq files include FPKM values for each Sample ...

source_name: Neural ectoderm

growth_protocol: Undifferentiated H9 cells were maintained on vitronectin-coated tissue culture dishes in mTeSR1 medium.A previously reported differentiation protocol was performed to induce H9 cells into neural ectoderm cells (Tchieu et al. 2017)

extract_protocol:
Total RNA was extracted with the Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 0.1% DMSO as control, or 1 μM BDE-47/BDE-209/TBBPA/TBBPS/TCBPA/MIXTURE.

tag: agent

value: mixture of BDE-47, BDE-209, TBBPA, TBBPS, TCBPA

value: embryo

tag: cell lie


title: TLCN132

description: Hepatocellular carcinoma


title: TLCN137

description: Hepatocellular carcinoma


title: TLCN139

description: Hepatocellular carcinoma


title: TCBPA_2

value: TCBPA


title: Biopsy_DBD_Non-EVLP_7


title: Biopsy_DBD_Non-EVLP_8


title: TBBPS_2

value: TBBPS


title: M_2


title: TCBPA_1


title: TBBPA_2

value: TBBPA


title: TLCN129

description: Hepatocellular carcinoma


title: TLCN134

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_6


title: TBBPA_1


title: Biopsy_DBD_Non-EVLP_3


title: TLCN128

description: Hepatocellular carcinoma


title: Biopsy_DBD_Non-EVLP_5


title: BDE-209_2


title: Vcan_asex2

city: Villeurbanne

first: Aurore

last: Gallot

address: 43 Bd du 11 novembre 1918

institute: Universite Lyon

data_processing:
trimming with trimmomatic
HiSat2 mapping
Differential analysis DESeq2

organism: Venturia canescens

growth_protocol: Just upon emergence adult females were decapited, heads collected and flash frozen

extract_protocol:
Rneasy Mini Kit with manufafacturer protocol including the Dnase step
Illumina TruSeq Stranded mRNA Library Prep kit
polyadenylated RNAs were enriched from 1 μg of high-quality total RNAs with oligo-dT magnetic beads

treatment_protocol: Pools of 30 heads were crushed using steel beads and TissueLyser

tag: gender

value: female

value: head

tag: group

value: asexual


title: BDE-47_2


title: BDE-47_1


title: Vcan_asex3


title: TLCN125

description: Hepatocellular carcinoma

value: HCV


title: TLCN126

description: Hepatocellular carcinoma


title: TBBPS_1


title: Vcan_asex1


title: Ctrl_2

value: control


title: Vcan_sex3

value: sexual


title: TLCN124

description: Hepatocellular carcinoma


title: TLCN123

description: Hepatocellular carcinoma


title: TLCN120

description: Hepatocellular carcinoma


title: Vcan_sex2


title: BDE-209_1


title: Vcan_sex1


title: TLCN116

description: Hepatocellular carcinoma


title: Ctrl_1


title: TLCN115

description: Hepatocellular carcinoma


title: TLCN110

description: Hepatocellular carcinoma


title: Control-3(empty adenovirus overexpression)

city: Harbin

first: Jiyuan

last: Zhu

address: Xiangfang District, No. 600 Changjiang Road

department: College of Animal Science and Technology

institute: Northeast Agricultural University

data_processing:
The raw data of RNA-SEQ includes splice sequences and sequenced low-quality sequences. In order to ensure the accuracy of information analysis, the sequenced raw data needs to be filtered to obtain clean data.(1) The reads linker was removed and the sequence length was less than 30 BP; (2) cut off the sequence of Q < 5 at the beginning and end of reads; (3) remove reads with Q < 15; (4) detect the quality of the sliding window with a width of 5bp for each sequence. If the average quality of a window is lower than 15, cut off the sequence after the window.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
High quality reads were mapped to reference genome of S. scrofa (11.1) using HISAT2 program .
Transcript abundances were quantified with StringTie software, and normalized with FPKM (Fragments per kilobase of transcript per million mapped reads) method across libraries.FPKM value was used to measure the gene expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Preadipocytes

growth_protocol: Subcutaneous fat tissues were obtained after the newborn Min pigs were slaugh-tered, washed with sterile phosphate-buffered saline (PBS), and potentially contami-nated muscle and connective tissue was carefully removed. After washing three times in PBS containing 1% penicillin–streptomycin (Invitrogen), fat tissues were cut into small pieces and digested with 0.1% type I collagenase (Invitrogen) for 40–50 min at 37℃, then mixed with equal volumes of culture medium supplemented with penicillin–streptomycin and 10% fetal bovine serum (FBS) (Sigma, St. Louis, MO, USA), and fil-tered through 400-mesh filters. The filtrates were centrifuged at 1000 rpm for 5 min. The cell precipitation was resuspended with Dulbecco’s modified Eagle’s medium/Nutrient Mixture F-12 (DMEM/F12) containing 10% FBS and 1% penicillin–streptomycin. The medium was changed every 2 days until cells were grown to a desired density.

extract_protocol:
subcutaneous adipose tissues were collected from newborn Min pigs to culture cells. RNA was extracted with TRIzol reagent (Invitrogen, CA, USA)A total of six Ribo-Zero RNA-sequencing libraries including overexpressing and control groups were constructed, each with three replicates.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The recombinant adenoviruses were constructed using the AdEasy system (Hanbio, Shang, China) . BP CDS were inserted into the shuttle plasmid containing an enhanced green fluorescent protein (EGFP) and cyto-megalovirus promoters using Kpn Ⅰ and Xho Ⅰ sites, and homologous recombina-tion was performed in E. coli BJ5183 with adenoviral backbone pAdEasy 1. The recom-binant adenovirus plasmid was packaged in HEK-293A cells after linearized with Pac Ⅰ. Preadipocytes were infected with adenovirus virions at multiplicity of infection (MOI) of 300. At 48 h post-infection, cells were collected for RNA-Seq with Illumina NovoSeq 6000 platform (Illumina, San Diego, CA, USA) by Geneseeq Technology (Nanjing, China) using pair-end sequencing strategy according to the manufacturer’s protocols. Cells treated with empty adenovirus were used as a control.

tag: cell type

value: Preadipocytes

tag: cell source

value: subcutaneous adipose tissue

tag: treatment

value: control groups（empty adenovirus overexpression）


title: BP-3(BP adenovirus overexpression)

value: BP groups(BP adenovirus overexpression)


title: TLCN109

description: Hepatocellular carcinoma

tag: etiology

value: wt


title: Control-2(empty adenovirus overexpression)


title: BP-2(BP adenovirus overexpression)


title: TLCN118

description: Hepatocellular carcinoma

tag: ctnnb1 status