title: HSC, cultured with ApoE for 3 days, rep.2

city: Kumamoto

first: Kenichi

last: Miharada

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description: ApoE HSC #2

data_processing:
Trimming, alignment, peak calling, and Quantification were performed by FASTX-toolkit, Bowtie2, MACS2, and HOMER, respectively.
Assembly: mm10
Supplementary files format and content: Peak files (.bigwig)

source_name: Bone marrow

extract_protocol:
2,500 to 5,000 cells were sorted into microtubes containing PBS supplemented with 2.5 % FBS. After sorting, the cells were centrifuged at 300 x g for 10 min at 4°C to pellet down, and the supernatant was removed. The cell pellets were washed with 1 x RSB and centrifuged at 500 x g for 5 min at 4°C. After removing the supernatant, the pellets were resuspended in cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.01 % digitonin, 0.1 % Tween-20, and 0.1 % NP-40) and incubated for 3 min on ice. Then 1 ml of wash buffer was added and centrifuged at 500 x g for 10 min at 4°C to pellet the nuclei.
The pellets were resuspended in a transposition reaction mix (2 μl transposase, 25 μl TD buffer, PBS, digitonin, Tween-20), and the transposition reaction was performed at 37°C for 1 hour. The samples were then purified using MinElute Reaction Clean Up kit (QIAGEN).

value: Bone marrow

value: CD150+CD34-cKit+ScaI+Lineage- cells

value: Cultured with 10 μg/ml ApoE for 3 days


title: DNA methylation array - Day 5 iPSC control Rep3_BS

status: Public on Aug 07 2024

type: genomic

city: Barcelona

first: Mercedes

last: Barrero

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

hyb_protocol: 1µg of each sample was evenly splitted for the oxidation reaction and the mock-oxidation reaction where the oxidant solution was replaced by water following the TrueMethyl oxBS Module manufacturer’s instructions (NuGEN-Tecan, 0414). Both aliquots were then processed in parallel for all stages of the protocol. After the oxidation reaction where 5-hydroxymethylcytosine is oxidized to 5-formylcytosine (5fC) and 5-methylcytosine (5mC) stays unchanged, the bisulfite treatment converts 5fC and all non-methylated cytosines to uracil, while 5mC is not altered. For samples to be run on the Illumina Infinium® Mouse Methylation BeadChip Array (Illumina, 20041558), 7 μL of recovered TrueMethyl template were mixed with 1 μL of 0.4 N NaOH following manufacturer’s instructions. All subsequent steps were completed following the Infinium HD Assay Methylation protocol  (https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium_hd_methylation/infinium-hd-methylation-guide-15019519-01.pdf).

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
IDAT files were preprocessed and analyzed using the minfi R package (v1.42.0). Probes were filtered for a detection p-value threshold of 0.01, and cross-reactive probes were removed. The remaining data was normalized using the preprocessQuantile method. Limma R package was used to do an experimental batch-correction.
Normalized beta values; normalization was done for array intensity using the preprocessQuantile method and then an experimental batch-correction was done using the Limma R package

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

source_name: Day 5 iPSC

label_protocol: Cy5 and Cy3

growth_protocol: Reprogramming was induced in the presence or absence of IFNγ (from day 0 to 5). SSEA1+ day 5 iPSCs (4 replicates from different reprogramming rounds) and SSEA1+ X-GFP+ day 7 iPSCs (2 replicates from different reprogramming rounds) were sorted by FACS.

extract_protocol: Genomic DNA was extracted and purified from reprogramming sorted cells using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Mouse recombinant IFNγ (10 ng/ml) (R&D Systems, 485-MI-100) was added to the reprogramming medium from day 0 to day 5.

tag: cell type

value: Day 5 iPSC

tag: treatment

value: D5 control


title: 528NS cells, shDHRS13 #2, Day 2

type: SRA

city: Seoul

first: Min Ji

last: Park

country: South Korea

institute: Korea University

description: Fold change_528NS-shNT vs shDHRS13 #2.xls

library_source: transcriptomic

data_processing:
Raw fragments per kilobase million (FPKM) and probability values (PA) were calculated using the performer’s algorithm and used for further analysis. Genes with PA > 0.8, whose expression levels increased or decreased by more than 2-fold after the knockdown of DHRS13, were grouped and designated as DEGs.
Assembly: mm10
Supplementary files format and content: Excel files include Log2(Fold Change) values and q-values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Brain

growth_protocol: 528NS and GSC11 cells were cultured in Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12) supplemented with 0.2% B27, 20 ng/mL epidermal growth factor (EGF), 20 ng/mL basic fibroblast growth factor (b-FGF), 1% penicillin/streptomycin, 2 mM L-glutamine, and 50 μg/mL gentamicin.

extract_protocol:
Total RNA was extracted from cells using QIAzol lysis reagent (Qiagen) according to the manufacturer’s instructions. RNase-free, DNase-treated RNA (1 μg) was used as the template.
RNA libraries for RNA-seq were prepared using Ditrct-zol™ RNA MiniPrep Kit following manufacturer's protocols.

tag: tissue

value: Brain

tag: cell line

value: Cancer stem-like cells

tag: genotype

value: DHRS13 knockdown


title: HSC, cultured with ApoE for 3 days, rep.1

description: ApoE HSC #1

library_source: genomic


title: gRNA sequencing -  Late Pluripotent Biol Rep1

data_processing:
The gRNA sequencing from the CRISPR KO screening was analyzed with MAGeCK software (Li et al. 2014). The gRNA abundance of each population was determined by taking into account the two biological replicates (with two technical replicates each). The gRNA abundance comparisons were performed pairwise.
Assembly: mm10
Supplementary files format and content: xlsx file containing raw counts for each gRNA in each sample

source_name: hybrid 129S1/SvImJ, CAST/EiJ

growth_protocol: Mouse embryonic stem cells were incubated at 37 °C with 5% CO2 and cultured on 0.2% gelatin-coated plates in serum/LIF medium: DMEM medium (Thermo Fisher Scientific, 31966021) supplemented with 10% FBS (ES pre-tested, Capricorn, FBS-ES-12A), 1,000 U/ml LIF (ORF Genetics, 01-A1140-0100), 25mM HEPES (Thermo Fisher Scientific, 15630056), 1mM Sodium Pyruvate (Thermo Fisher Scientific, 11360070), 1x MEM NEAA (Thermo Fisher Scientific, 11140050), 50U/ml penicillin/streptomycin (Ibian Tech, P06-07100) and 0.1mM 2-mercaptoethanol (Thermo Fisher Scientific, 31350010). Neural Precursor cells were differentiated from ESCs and cultured in RHBA medium (Takara Bio, Y40001) supplemented with 10 ng/ml EGF (R&D Systems, 236-EG-200), 10 ng/ml bFGF (Thermo Fisher Scientific, 13256029) and ROCK inhibitor 10 µM (Selleck Chemicals, S1049). Cells undergoing reprogramming were grown on top of male irradiated Mouse Embryonic Fibroblasts (iMEFs) on 0.2% gelatin coated plates in iPSC medium: DMEM medium (Thermo Fisher Scientific, 31966021) supplemented with 15% FBS (ES pre-tested, Capricorn, FBS-ES-12A), 25mM HEPES (Thermo Fisher Scientific, 15630056), 1mM Sodium Pyruvate (Thermo Fisher Scientific, 11360070), 1x MEM NEAA (Thermo Fisher Scientific, 11140050), 50U/ml penicillin/streptomycin (Ibian Tech, P06-07100) and 0.1mM 2-mercaptoethanol (Thermo Fisher Scientific, 31350010), supplemented with 1,000 U/ml LIF, 25 mg/ml L-ascorbic acid and 1 mg/ml doxycycline.

extract_protocol:
Cells were dissociated and sorted based on BFP, SSEA1-APC and X-GFP expression using a BD FACSAria II SORP.
Genomic DNA was extracted from cell pellets using the DNeasy Blood and Tissue Kit (Qiagen, 69504). For amplification of the gRNAs and introduction of the Illumina-sequencing adapters, two consecutive PCRs were performed by using the Q5 High-Fidelity DNA Polymerase (NEB, M0491), adding the Illumina adapsters for NGS.
Single-end sequencing (1 x 50 bp) on an Illumina HiSeq 2500. Each sample contains two technical replicates

value: hybrid 129S1/SvImJ, CAST/EiJ

value: reprogramming cell

value: Late Pluripotent


title: gRNA sequencing -  Early Pluripotent Biol Rep2

value: Early Pluripotent


title: 528NS cells, shDHRS13 #1, Day 2

description: Fold change_528NS-shNT vs shDHRS13 #1.xls


title: HSC, cultured with DMSO for 3 days, rep.2

description: Ctrl HSC #2

value: Cultured with DMSO for 3 days


title: DNA methylation array - Day 5 iPSC IFNg Rep2_BS

value: D5 IFNg


title: DNA methylation array - Day 5 iPSC control Rep3_BS_OX


title: HSC, cultured with DMSO for 3 days, rep.1

description: Ctrl HSC #1


title: 528NS cells, shNT, Day 2

description:
Fold change_528NS-shNT vs shDHRS13 #1.xls
Fold change_528NS-shNT vs shDHRS13 #2.xls

value: WT


title: gRNA sequencing -  Non-Pluripotent Biol Rep2

value: Non-Pluripotent


title: DNA methylation array - Day 5 iPSC IFNg Rep2_BS_OX


title: gRNA sequencing -  Early Pluripotent Biol Rep1


title: HSC, freshly isolated, rep.2

description: Fresh HSC #2


title: RNA-seq - ESC Rep 2

data_processing:
FastQ files passing the quality control were aligned to the mm10 reference genome, which contained CAST/EiJ and 129S1/SvImJ SNPs positions masked. The SNPs positions of the mouse strains were obtained fromftp://ftp-mouse.sanger.ac.uk/REL-1505-SNPs_Indels/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi. A VCF file containing only the SNPs positions from CAST/EiJ and 129S1/SvImJ strains was generated. Alignment of reads to the reference genome was done using STAR (Dobin et al. 2013) with implementation of the WASP method (van de Geijn et al. 2015) to filter allele specific alignments. The output BAM files were used to obtain the read counts using the HTseq tool (v0.6.1) (Anders, Pyl, and Huber 2015). These steps were performed using a published Nextflow pipeline (Di Tommaso et al. 2017) and following the workflow described in https://github.com/biocorecrg/allele_specific_RNAseq. Read counts were normalized to library size using DESeq2 R package.
Assembly: mm10
Supplementary files format and content: txt file of non-allelic normalized expression counts of RNA-seq data obtained with DESeq2
Supplementary files format and content: txt file of allelix ratio (X mus proportion) of X-linked genes expressed on X cas (over 25% of total expression)

extract_protocol:
Cells were dissociated and sorted based on SSEA1-APC and X-GFP expression. Cell pellets were frozen at -80ºC until processed. RNA was extracted from cell pellets by using a RNeasy Plus Mini Kit (Qiagen, 74136) or RNeasy Micro Kit (Qiagen, 74004).
RNA libraries preparation was performed by ribosomal RNA depletion using the TruSeq Stranded Total RNA Library Preparation Kit (Illumina, 20020596)
Paired-end sequencing (2 x 50 bp) on an Illumina HiSeq 2500.

value: embryonic stem cell

value: ESC


title: gRNA sequencing -  Non-Pluripotent Biol Rep1


title: HSC, freshly isolated, rep.1

description: Fresh HSC #1

value: Bone marrow

value: CD150+CD34-cKit+ScaI+Lineage- cells


title: VLDLR-pos HSC, PHZ-injected, rep.2

description: PHZ VLDLR-pos HSC #2


title: DNA methylation array - Day 5 iPSC control Rep2_BS_OX

value: Day 5 iPSC


title: gRNA sequencing -  NPC Biol Rep2

value: neural precursor cell

value: NPC


title: VLDLR-pos HSC, PHZ-injected, rep.1

description: PHZ VLDLR-pos HSC #1


title: gRNA sequencing -  NPC Biol Rep1


title: Pool, NaCl, DOX, Set2, BioRep C

city: Toronto

first: Emily

middle: Haochen

last: Xiong

state: Ontario

address: 101 College Street

department: Department of Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Barcode sequence reads were mapped to an artificial genome containing known UPTAG and DNTAG sequences via Bowtie.
Assembly: Barcode sequence reads were mapped to an artificial genome containing known UPTAG and DNTAG sequences of pooled strains via Bowtie. Read frequency for the UPTAG and DNTAG of each strain were compiled for each indexed sample.
Supplementary files format and content: Single merged comma-seperated file with UPTAG and DNTAG barcode counts for all genes using summed values from all raw sequencing files of each sample
Library strategy: Bar-Seq

organism: Candida albicans

source_name: GRACE mutants in CaSS1 background

growth_protocol: Stock pools were thawed, diluted into 24-well plates (Falcon, 353047) in triplicate 1 ml cultures to an OD600 of 0.05 with or without 100 µg/mL DOX. Cultures were incubated for 24 hours in a static manner in the conditions of interest or until OD600 of cultures reached approximately 5.0 (File S1). The cultures were each sub-cultured into triplicate 1 ml cultures with fresh medium at an OD600 of 0.05 with or without 100 µg/mL DO

extract_protocol:
Genomic DNA was purified using the PureLinkTM Genomic DNA Mini Kit as per instructions with minor modifications, as described. Cell pellets were resuspended in 400 µL of lysis buffer (from PureLink Kit) and physically lysed by adding approximately 200 uL of acid-washed glass beads and bead beating six times for 30 seconds. Extracted genomic DNA was quantified with the Quant-iTTM PicoGreen dsDNA Assay Kit.
Barcode amplification by PCR was performed using 105.6 ng of genomic DNA via the Ex-Taq enzyme UPTAG and DNTAG primer sequences are included in File S5 of associated paper. Separate UPTAG and DNTAG multiplexed pools were formed by combining equal amounts of PCR product from each sample. Pooled UPTAG and DNTAG DNA pools were extracted from a 1% agarose gel using the QIAquick® Gel Extraction Kit. Equal quantities of UPTAG and DNTAG pools as determined by PicoGreen assay were combined to form a library, which was sequenced on an Illumina MiSeq v2 Regular or NextSeq v2.5 Mid-Output instrument (single-end flow cell) using specific primers to sequence and index the UPTAG and DNTAGs (File S5).

treatment_protocol: We screened the barcoded GRACE collection in the baseline condition of synthetic defined YNB medium at 30 °C, as well as six additional growth conditions at 30 °C including: nutrient-rich medium (YPD), YNB containing the osmotic stressor sodium chloride (NaCl), YNB supplemented with serum—a key component in human blood, YNB supplemented with the membrane stressor sodium dodecyl sulfate (SDS), YNB containing the osmotic stressor sorbitol, and iron-free YNB; we also screened in YNB at the elevated temperature of 37 °C. Full Protocol can be found in associated paper.

value: GRACE mutants in CaSS1 background

tag: genetic modification

value: For each strain, one allele of the target gene is deleted using a HIS3 cassette and the other is placed under the regulation of a tetracycline-repressible promoter which allows gene expression to be repressed by the addition of a tetracycline analog, doxycycline.

tag: time

value: 40h, subculture into fresh media, then 72h

tag: strain

value: Pooled culture of GRACE library strains

value: 100 µg/mL DOX

tag: condition

value: YNB with 1M NaCl at 30 C


title: NY-7-2

type: RNA

city: Tokyo

first: Kazuyuki

last: Ishihara

address: 2-1-14 Kanda-Misakicho, Chiyoda-ku

department: Microbiology

institute: Tokyo Dental College

hyb_protocol: cRNA was hybridized to a 15K 60-mer oligomicroarray (Treponema denticola custom Microarray 8x16K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction 12.0.3.1 (Agilent Technologies).

data_processing: The fluorescent intensity data extracted from the raw images were imported into Agilent Feature Extraction 12.0.3.1 (Agilent Technologies). After per chip normalization (Shift to 75 percentile) and per gene normalization (mean of control samples) were performed with GeneSpring 13.1.1.

organism: Treponema denticola

source_name: oxtR deficient mutant

label_protocol: The cRNA was amplified, labeled using Low Input Quick Amp WT Labeling Kit according to the manufacturer's instructions.

growth_protocol: T. denticola ATCC 35405 or NY-7 were inoculated into 100 mL 10% TYGVS and incubated at 37°C under anaerobic conditions for 2 d (to an absorbance at 660 nm of approximately 0.4-0.6).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) according to the manufacturer's instructions.

treatment_protocol:
Td 35405: T. denticola ATCC 35405 grown in medium containing 10% serum.
Td NY-7: T. denticola NY-7 grown in medium containing 10% serum.

value: oxtR deficient mutant


title: VLDLR-neg HSC, PHZ-injected, rep.2

description: PHZ VLDLR-neg HSC #2


title: DNA methylation array - Day 5 iPSC IFNg Rep1_BS_OX

value: D5 IFNg


title: IkE5_PMA_Treg_3

city: Suita

first: Kenji

last: Ichiyama

state: Osaka

address: 3-1 Yamadaoka

institute: Osaka University

data_processing:
Gene expression was quantified using ikra (v2.0), v2.0), an RNA-seq pipeline centered on Salmon.
Sequence reads were executed the following tools for the quality control, trimming, and quantification of transcripts; Trim Galore (v0.6.6), Salmon (v1.4.0), and tximport (v1.6.0),  consequently outputting the scalled TPM and TPM values.
The differentially expressed genes were identified by DEseq2 in iDEP (v0.90) using the scalled TPM values.
Assembly: GENCODE vM26
Supplementary files format and content: Text files include scalled TPM and TPM values for each Sample, respetively.

source_name: Spleen and Lymphnodes

extract_protocol:
RNA was harvested using RLT buffer (Qiagen) containing 1% 2-mercaptoethanol, followed by RNA reverse transcription by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech).
After enzymatic fragmentation of cDNA samples by KAPA Frag kit (KAPA Biosystems), sequencing libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems).

treatment_protocol: Purified Treg cells were stimulated with Cell Stimulation Cocktail for 2hrs  in RPMI 1640  supplemented with 10% fetal calf serum (FCS), 2-mercaptoethanol and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

value: Spleen and Lymphnodes

value: Primary

value: Treg cells

value: Cell Stimulation Cocktail for 2hrs


title: NY-7-1


title: VLDLR-neg HSC, PHZ-injected, rep.1

description: PHZ VLDLR-neg HSC #1

value: Bone marrow


title: IkE5_PMA_Treg_2


title: DNA methylation array - Day 5 iPSC control Rep1_BS

value: D5 control


title: Pool, NaCl, DOX, Set2, BioRep B


title: Pool, NaCl, DOX, Set2, BioRep A


title: VLDLR-pos HSC, Steady-state, rep.2

description: SS VLDLR-pos HSC #2


title: IkE5_PMA_Treg_1


title: DNA methylation array - Day 5 iPSC control Rep1_BS_OX

value: Day 5 iPSC


title: Pool, NaCl, NO DOX, Set2, BioRep C

value: No DOX


title: WT_PMA_Treg_3

value: WT


title: VLDLR-pos HSC, Steady-state, rep.1

description: SS VLDLR-pos HSC #1


title: Pool, NaCl, NO DOX, Set2, BioRep B

value: GRACE mutants in CaSS1 background


title: WT_PMA_Treg_2


title: DNA methylation array - Day 5 iPSC IFNg Rep1_BS


title: Pool, NaCl, NO DOX, Set2, BioRep A

value: For each strain, one allele of the target gene is deleted using a HIS3 cassette and the other is placed under the regulation of a tetracycline-repressible promoter which allows gene expression to be repressed by the addition of a tetracycline analog, doxycycline.


title: VLDLR-neg HSC, Steady-state, rep.1

description: SS VLDLR-neg HSC #1


title: DNA methylation array - Day 5 iPSC control Rep2_BS


title: WT_PMA_Treg_1


title: SetDB1-WT_Input_rep2

status: Public on Aug 06 2024

city: Changsha

first: Ruijun

last: Tang

address: No. 97 Xiangya Road

country: China

institute: Xiangya Hospital Central South University

data_processing:
Illumina Casava1.8 software was used for basecalling.
For ChIP-seq and RNA-seq, The raw sequenced reads were cleaned using trim_galore (v0.6.0) with default parameters, and then mapped to the reference D. melanogaster genome (dm6, version BDGP6).
For ChIP-seq, Using Bowtie2 (v2.3.5.1) with the default parameters that look for multiple alignments but only report the one with the best mapping quality. For RNA-seq, The key alignment parameters were as follows: “--outFilterMismatchNoverLmax 0.04  --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 500 --outMultimapperOrder Random --outSAMmultNmax 1”
For ChIP-seq, Peak calling was performed using MACS2 v2.2.6 (parameters: -g dm --nomodel --broad --broad-cutoff 0.1). For RNA-seq, Genes expression was quantified using featureCounts v1.6.5 based on dm6 RefSeq genes annotation file.
For ChIP-seq, Bigwig tracks were generate using bamCoverage from deeptools (parameters: -b ChIP_dm6_sorted.bam -o ChIP_dm6.bw -scaleFactor a -bs 200 -p 4). The ChIP-Seq profiles were generated by computeMatrix and plotHeatmap in deepTools. IGV v.2.9.2 was used to visualize the bigwig tracks. For RNA-seq, Differential expression analysis was performed based on the negative binomial distribution using R package edgR.
Assembly: dm6
Supplementary files format and content: bw files were generated using bamCoverage.
Supplementary files format and content: peak excel files.
Supplementary files format and content: In ChIP-seq, the normalized signals by spike-in for every sample .In RNA-seq, CPM table for every gene and every sample.

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
Embryos lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies. And 100ng total RNA was harvested using Trizol reagent from a single embryo.
The sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: embryos

value: ; GFP-SetDB1 WT/CyO;


title: SetDB1-WT_Input_rep1


title: SetDB1-WT_H3K9me3_rep2

value: H3K9me3 ChIP antibody


title: SetDB1-F578A_H3K9me3_rep2

value: ; GFP-SetDB1 F578A/CyO;


title: SetDB1-F578A_GFP-SetDB1_rep2

value: GFP ChIP antibody


title: SetDB1-WT_GFP-SetDB1_rep1


title: SetDB1-F578A_Input_rep1


title: SetDB1-WT_H3K9me3_rep1


title: SetDB1-F578A_Input_rep2


title: Rat kidney thallium 5 days

first: Toshihiko

last: Aki

address: 1-5-45 Yushima

department: Forensic medicine

institute: Tokyo Medical and Dental University

description: RNA expression value

hyb_protocol: Hybridization was performed according to the manufacturer's instruction.

scan_protocol: Array scanning was performed according to the manufacturer's instruction.

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization.

label: biotin

organism: Rattus norvegicus

source_name: Spleen

label_protocol: Labeling was performed according to the manufacturer's instruction.

extract_protocol: RNA was isolated from rat spleen with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: 40 mg/kg thallium was injected i.p. to rats daily for 2 or 5 days.

tag: Sex

value: male


title: SetDB1-F578A_H3K9me3_rep1


title: SetDB1-F578A_GFP-SetDB1_rep1


title: 405-2

organism: Treponema denticola ATCC 35405

source_name: Wild type

value: Wild type


title: RNA-seq of SetDB1 WT stage 5 embryos repeat 3

value: ; SetDB1 WT;


title: RNA-seq of SetDB1 WT stage 5 embryos repeat 2


title: VLDLR-neg HSC, Steady-state, rep.2

description: SS VLDLR-neg HSC #2


title: RNA-seq of SetDB1 WT stage 5 embryos repeat 1


title: 405-1


title: RNA-seq of SetDB1 F578A stage 5 embryos repeat 3

value: ; SetDB1 F578A/CyO;


title: RNA-seq of SetDB1 F578A stage 5 embryos repeat 1


title: RNA-seq of SetDB1 F578A stage 5 embryos repeat 2


title: Rat kidney thallium 2 days

description: RNA expression value


title: stage6_H3K9me2-3_Input


title: SetDB1-WT_GFP-SetDB1_rep2


title: stage6_H3K9me2

value: H3K9me2 ChIP antibody


title: stage6_H3K14ac

value: H3K14ac ChIP antibody


title: stage5_H3K9me3


title: stage6_H3K14ac_Input


title: Lhx2

city: Setagaya-ku

last: Kitajima

state: Tokyo

address: 2–1-6 Kamikitazawa

department: Stem Cell Project

institute: Tokyo Metropolitan Institute of Medical Science

description: Gene expression

hyb_protocol: According to the Agilent Gene Expression Hybridization Kit protocol, 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized on an Agilent Human GE 4x44K v2 Microarray  for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5 µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: K562 cells were cultured in RPMI/10%FCS for 3 days.

extract_protocol: Total RNA was extracted by RNeasy mini kit (Qiagen) as manufacture's recommendations

treatment_protocol: K562 cells were transduced with empty vector and Lhx2 expression vector.

value: Lhx2 OE


title: Rat kidney control

description: RNA expression value


title: EGFP

description: Gene expression

value: empty vector


title: stage5_H3K14ac_Input


title: stage4_H3K9me2


title: stage5_H3K9me2-3_Input


title: stage4_H3K14ac_Input


title: stage4_H3K9me2-3_Input


title: stage4_H3K14ac


title: H3K9me3 ChIP-seq of w knock-down stage 5 embryos repeat 2

value: ; GFP-SetDB1, nos-Gal4; w RNAi


title: stage4_H3K9me3


title: stage5_H3K14ac


title: H3K14ac ChIP-seq of w knock-down stage 5 embryos repeat 2


title: H3K14ac ChIP-seq of w knock-down stage 5 embryos repeat 1


title: input genomic DNA of w knock-down stage 5 embryos repeat 2


title: H3K9me3 ChIP-seq of w knock-down stage 5 embryos repeat 1


title: input genomic DNA of w knock-down stage 5 embryos repeat 1


title: stage6_H3K9me3


title: GFP-SetDB1 ChIP-seq of w knock-down stage 5 embryos repeat 2


title: GFP-SetDB1 ChIP-seq of w knock-down stage 5 embryos repeat 1


title: input genomic DNA of Gcn5 knock-down stage 5 embryos repeat 1

value: ; GFP-SetDB1, nos-Gal4; Gcn5 RNAi


title: H3K9me3 ChIP-seq of Gcn5 knock-down stage 5 embryos repeat 2


title: input genomic DNA of Gcn5 knock-down stage 5 embryos repeat 2


title: H3K14ac ChIP-seq of Gcn5 knock-down stage 5 embryos repeat 2


title: stage5_H3K9me2


title: H3K14ac ChIP-seq of Gcn5 knock-down stage 5 embryos repeat 1


title: GFP-SetDB1 ChIP-seq of Gcn5 knock-down stage 5 embryos repeat 2


title: RNA-seq of w knock-down stage 5 embryos repeat 1


title: RNA-seq of w knock-down stage 5 embryos repeat 2


title: RNA-seq of w knock-down stage 5 embryos repeat 3


title: GFP-SetDB1 ChIP-seq of Gcn5 knock-down stage 5 embryos repeat 1


title: RNA-seq of Gcn5 knock-down stage 5 embryos repeat 2


title: Normal_pt3 [S96_L001, S96_L002]

first: Jaemoon

last: Koh

state: Seoul

address: Jongnogu 101 Seoul National University hospital, B1, Department of Pathology

institute: Seoul National University Hospital

library_source: other

data_processing:
Library strategy: Spatial Trtanscriptomics
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads
Sequencing reads were mapped to the hg38 human using STAR v2.7.3a
Gene level abundance was quantitated from the filtered human alignments in R using the GenomicAlignments Bioconductor package (version 1.22.1)
Assembly: hg38
Supplementary files format and content: digital count conversion (.dcc) file

source_name: Lung

extract_protocol:
RNA extracted by column purification using an RNA isolation kit Rneasy (Qiagen) according to the manufacturer's protocol
RNAseq libraries were constructed from 1ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit

value: Lung

tag: disease state

value: Normal

value: B lymphocyte

value: wt


title: Normal_pt3 [S95_L001, S95_L002]

value: T lymphocyte


title: Normal_pt1 [S90_L001, S90_L002]

value: macrophage


title: Normal_pt1 [S92_L001, S92_L002]


title: Normal_pt3 [S94_L001, S94_L002]


title: Normal_pt2 [S93_L001, S93_L002]

value: stromal cells


title: Normal_pt1 [S91_L001, S91_L002]


title: NTM_pt6 [S85_L001, S85_L002]

value: nontuberculous mycobacterial lung disease


title: NTM_pt6 [S87_L001, S87_L002]


title: Normal_pt1 [S89_L001, S89_L002]


title: NTM_pt6 [S86_L001, S86_L002]


title: NTM_pt6 [S88_L001, S88_L002]


title: NTM_pt6 [S82_L001, S82_L002]


title: NTM_pt6 [S84_L001, S84_L002]


title: NTM_pt6 [S81_L001, S81_L002]


title: NTM_pt6 [S83_L001, S83_L002]


title: H3K9me3 ChIP-seq of Gcn5 knock-down stage 5 embryos repeat 1

value: embryos

value: H3K9me3 ChIP antibody


title: sp_2dpf_wt_B_ATACseq

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

country: Italy

institute: Stazione Zoologica Anton Dohrn

description:
tagmented DNA
sp_2dpf_OCRs.tsv

data_processing:
scRNA-seq:
scRNAseq FASTQ reads were aligned to S. purpuratus genome version 3.1 using Cell Ranger 3.0.2 (10x Genomics).
Cell Ranger output files for all the replicates were used in Seurat v3.0.2 R package.
Genes transcribed in less than three cells and cells with less than 200 transcribed genes were excluded.
Datasets were normalized and variable genes were found using vst method with maximum 2000 variable features.
Data was integration was performded using anchors between the six different objects.
Data was scaled and principal component (PCA) analysis was performed. Sharing Nearest Neighbor (SNN) was computed with 20 dimensions (resolution 1.0). UMAP was used to perform clustering dimensionality reduction.
Positive cluster markers were found using the genes that are detected in at least 0.01 fraction of min.pct cells.
ATAC-seq:
ATACseq FASTQ reads were trimmed using Trimmomatic 0.38 with ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:6 CROP:40 SLIDINGWINDOW:3:25 MINLEN:25 settings.
Trimmed reads were mapped to S. purpuratus genome version 3.1 using bowtie2 2.3.4.1.
Resulting bam files were filtered to have fragments of less than 130, with quality over 30, mates were fixedd and duplicates removed using samtools 1.7.1. Then bam files were converted into bed using bedtools 2.27.1.
MACS2 2.1.2 was used for peak-calling with --extsize 100, --shift 50, --nomodel settings with genome size of 815936258.
Bedtools 2.27.1 intersect and merge were used to keep regions in both replicates per sample and merge peaks from gut and whole embryo samples.
Assembly: S. purpuratus genome 3.1
Supplementary files format and content: R object file, tab separated values

organism: Strongylocentrotus purpuratus

source_name: 2dpf gastrula whole embryo

growth_protocol: AdultStrongylocentrotus purpuratus were kept in circulating seawater aquaria at Stazione Zoologica Anton Dohrn in Naples. Spawning was induced by vigorous shaking of adult animals. Embryos were cultured at 15 °C in filtered Mediterranean Sea water diluted 9:1 with deionized water.

extract_protocol:
For scRNAseq embryos were collected using a 40 μm Nitex mesh filter and spun down at 500 g for 5 min. Sea water was removed and embryos were resuspended in Ca2+ Mg2+-free artificial sea water, then spun down at 500 g for 5 min and resuspended in dissociation buffer (1 M glycine and 0.02 M EDTA in Ca2+ Mg2+-free artificial sea water). Embryos were incubated for 10 min on ice and dissociated gently via pipette aspiration. Dissociated cells were spun down at 700 g for 5 min and washed several times with Ca2+ Mg2+-free artificial sea water.
scRNA-seq: Single cell cDNA libraries were prepared using the Chromium Single Cell 3’ Reagent Kit, Chemistry v3 and v3.1.
scRNA-seq: Libraries were indexed, multiplexed and sequenced on Illumina NextSeq 500 to generate paired end reads.
For ATACseq Embryos were collected using a 40 μm Nitex mesh filter and spun down at 500 g for 5 min. For gut tissue sea water was removed and embryos were resuspended in Ca2+ Mg2+-free artificial sea water, then spun down at 500 g for 5 min and resuspended in dissociation buffer (1 M glycine and 0.02 M EDTA in Ca2+ Mg2+-free artificial sea water); embryos were incubated for 10 min on ice and then continuously pipetted up and down with P1000 micropipette to mechanically separate the gut tissue. Separated guts were collected in 100  μl of artificial sea water on ice. The guts or whole embryos were washed in 4 °C artificial sea water, the lysed in 50 μl of 10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% IGEPAL CA-630 lysis buffer. Nuclei were centrifuged at 500g, supernatant discarded. 75000 nuclei were tagmented in 2x tagmentation buffer (20 mM Tris-HCl, 10 mM MgCl2, 20% (vol/vol) dimethylformamide), 23.75 μl of nuclease free water and 1.25 μl of Tn5 enzyme from Dr Jose Luis Gómez-Skarmeta.
ATAC-seq: The tagmented DNA was purified using MinElute Kit (Qiagen) and eluted in 10 μl of elution buffer, and amplified (10 μl of eluted tagmented DNA, 10 μl of nuclease free water, 2.5 μl 10 μM Nextera Primer 1, 2.5 μl 10 μM Nextera Primer 2.X with following program: 72°C for 5 min, 98°C for 30 sec, then 15 cycles of 98 °C for 10 sec, 63 °C for 30 sec and 72 °C for 1 min, followed by a hold step at 4°C). The resulting library was purified using MinElute Kit (Qiagen) and eluted in 20 μl of elution buffer.
ATAC-seq: Indexed libraries were multiplexed and sequenced on Illumina HiSeq 4000 at  BGI Tech (HongKong) to generate paired end reads.

value: 2dpf gastrula whole embryo

tag: developmental stage

value: 2dpf gastrula

value: 2 dpf


title: NTM_pt5 [S79_L001, S79_L002]


title: NTM_pt5 [S78_L001, S78_L002]


title: sp_2dpf_wt_A_ATACseq

description:
tagmented DNA
sp_2dpf_OCRs.tsv


title: sp_2dpf_gut_B_ATACseq

description:
tagmented DNA
sp_2dpf_OCRs.tsv

source_name: 2dpf gastrula emrbyo gut

value: 2dpf gastrula emrbyo gut

value: 2dpf gastrula emrbyo gut tissue


title: RNA-seq of Gcn5 knock-down stage 5 embryos repeat 3


title: NTM_pt5 [S77_L001, S77_L002]


title: RNA-seq of Gcn5 knock-down stage 5 embryos repeat 1


title: GM12878_sgWAPL_3

city: Boston

first: Benjamin

last: Gewurz

state: MA

address: 181 Longwood Avenue, Channing Laboratory, 8th Floor

country: USA

institute: Brigham and Women's Hospital

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly and Akata EBV transcriptome
Salmon (v1.0.0) was used to quantify the transcripts, and DESeq v1.14.1 was used to determine differentially expressed genes. Genes that had a log2(fold change) of at least 1 and an adjusted p-value of < 0.05 were considered significant. Heatmaps were generated using Morpheus, and Enrichr was used to conduct gene ontology enrichment analysis.
Assembly: GRCh37.83 (hg19), Akata EBV
Supplementary files format and content: Excel sheets of the log2FC data are provided.

molecule: polyA RNA

growth_protocol: Human MUTU I and GM12878 cells were cultured in RPMI (Life Technologies) with 10% FBS and 1% penicillan/streptomycin at 37 degrees C and 5% CO2.

extract_protocol:
Total RNA was isolated using a Qiagen RNeasy extraction kit. An on-column DNA digestion was performed to remove any genomic DNA contamination.
For library preparation, 1 µg of RNA was used for each sample, polyA-enrichment was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs), and library construction was completed using NEBNext Ultra RNA Library Prep Kit for Illumina (#E7760L, New England Biolabs) as per the manufacturer’s instructions.

treatment_protocol: Human MUTU I and GM12878 cells expressing Cas9 were transduced with lentivirus for sgControl or sgWAPL and samples were collected post selection with puromycin.

value: B cells

tag: biomaterial provider

value: WAPL KO


title: NTM_pt5 [S75_L001, S75_L002]

value: Lung


title: NTM_pt5 [S80_L001, S80_L002]


title: GM12878_sgControl_1

value: control


title: NTM_pt5 [S74_L001, S74_L002]


title: NTM_pt4 [S71_L001, S71_L002]


title: MUTUI_sgWAPL_2

source_name: MUTU I

value: MUTU I


title: MUTUI_sgWAPL_3


title: NTM_pt4 [S68_L001, S68_L002]

value: B lymphocyte

value: wt


title: NTM_pt4 [S70_L001, S70_L002]

value: macrophage


title: MUTUI_sgWAPL_1


title: GM12878_sgControl_2


title: NTM_pt4 [S69_L001, S69_L002]

value: stromal cells


title: NTM_pt4 [S67_L001, S67_L002]

value: nontuberculous mycobacterial lung disease

value: T lymphocyte


title: NTM_pt4 [S66_L001, S66_L002]


title: NTM_pt5 [S76_L001, S76_L002]


title: NTM_pt4 [S65_L001, S65_L002]


title: sp_2dpf_gut_A_ATACseq

description:
tagmented DNA
sp_2dpf_OCRs.tsv


title: MUTUI_sgControl_2


title: MUTUI_sgControl_1


title: MUTUI_sgControl_3


title: NTM_pt4 [S63_L001, S63_L002]


title: WAPLKO_B

data_processing:
*library strategy: HiChIP
HiChIP data analysis of each sample was performed as previously described (16). Briefly, reads of biological replicates were processed with the HiC-Pro v3.1.0 pipeline (17) against a MboI digested hg19 with EBV genome build. For the human genome, Hichipper v0.7.7 (18) (parameter: EACH, ALL) was used to identify long-rang chromatin interactions based on valid HiChIP read pairs selected by HiC-Pro. Differential analysis of long-range interactions was performed by the diffloop v1.24.0 (19). Loop biases were filtered based on the binomial model described by mango using mangoCorrection (20). Loops with FDR < 0.01 and range > 5kb were kept for differential analysis. Differential loops between two conditions were estimated by considering reproducibility across replicate samples using quickAssocVoom. Significant differential loops (adjusted p-value < 0.05) were selected for visualization. For the EBV genome, genomic bins of 1500 bps length were treated as potential loop anchors. All pair-wise combinations of bins were quantified for their strength of potential interactions using HiChIP read pairs supporting the interacted two bins. Only read pairs labeled as allValidPairs by HiC-Pro were selected for quantification. Neighbored bin pairs and bin pairs with zero quantification in all samples were removed. DESeq2 v1.36.0 (14) was used to test differential loops based on quantification difference between two conditions. Significant differential loops (adjust p-value < 0.05) were visualized by circlize v0.4.15 R package (21).
Assembly: hg19
Supplementary files format and content: Excel sheets of the log2FC data are provided.

source_name: MUTU I cell line

growth_protocol: Human MUTU I  cells were cultured in RPMI (Life Technologies) with 10% FBS and 1% penicillan/streptomycin at 37 degrees C and 5% CO2.

extract_protocol:
10 million cells were collected and crosslinked with freshly made 1% formaldehyde, and crosslinking was quenched with 125 mM glycine. Crosslinked cells were lysed with iced-cold Hi-C lysis buffer at 4°C for 30 minutes with rotation. Pelleted nuclei were harvested and digested with 375U of MboI restriction enzyme (NEB, R0147) at 37°C for 2 hours with rotation.
Next, DNA ends were filled in and marked with biotin-dATP (Thermo, 19524016). T4 DNA ligase (NEB, M0202) was used for proximity ligation at room temperature for 4 hours with rotation. After ligation, pelleted nuclei were lysed with iced-cold nuclear lysis buffer and sonicated with Covaris M220 for 240 seconds. ChIP dilution buffer was used to dilute each sample to achieve a SDS concentration of 0.1%. After preclearing with Protein A magnetic beads, 7.5 µg of anti-H3K27ac antibody (abcam, ab4729) were added for every 10 million cells and incubated overnight at 4°C. Protein A magnetic beads were used to capture DNA-protein complexes. Beads were washed (three times each in Low Salt Wash Buffer, High Salt Wash Buffer, and LiCl Wash Buffer) and DNA was eluted in Elution Buffer. Crosslinks were then reversed via Proteinase K digestion, and DNA was purified with the QIAquick PCR purification kit (Qiagen). Samples were prepared for sequencing using the  Illumina Tagment DNA  Enzyme and Buffer Kits (Illumina, 20034197) per the manufacturer’s instructions.

treatment_protocol: Human MUTU I cells expressing Cas9 were transduced with lentivirus for sgControl or sgWAPL and samples were collected post selection with puromycin.

value: MUTU I cell line


title: NTM_pt4 [S64_L001, S64_L002]


title: NTM_pt4 [S62_L001, S62_L002]


title: GM12878_sgWAPL_2


title: WAPLKO_C


title: GM12878_sgWAPL_1


title: NTM_pt4 [S72_L001, S72_L002]


title: GM12878_sgControl_3


title: NTM_pt3 [S60_L001, S60_L002]


title: NTM_pt5 [S73_L001, S73_L002]


title: control_B


title: control_A


title: NTM_pt3 [S57_L001, S57_L002]


title: sp_2dpf_2a_scRNAseq

library_source: transcriptomic single cell

source_name: dissociated 2dpf gastrula embryo

value: dissociated 2dpf gastrula embryo

value: 2dpf gastrula cells


title: nirB transposon replicate 2

city: Princeton

first: Jacob

last: Marogi

state: Nj

address: Lewis Thomas Laboratory

institute: Princeton University

data_processing:
Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.1.5)
Assembly: Read mapping was performed with HISAT21. Read quantification was performed using Subread’s feature Counts2 functionality.
Supplementary files format and content: quantified gene data listed in allquantifiedgenesprocesseddata.xlsx

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: PA14 strains were grown for 16h at 37·C shaken in LB. Cultures were backdiluted to OD600 = 1 and lawns were plated on NGM plates, dried, and incubated for 2 days @ 25 °C.

extract_protocol:
Cultures were pelleted at 4°C, resuspended in Trizol (Ambion 10296010), and incubated at 65°C before addition of chloroform. The aqueous layer was collected and RNA was isolated using a mirVana RNA extraction kit (ThermoFisher AM1560). DNAse treatment was performed on RNA using recombinant DNase I (Sigma-Aldrich 04716728001).
RNA samples were sent to Seq Center (Pittsburg, PA) for sequencing using the Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion.
Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).

treatment_protocol: No treatment

value: bacteria

value: nirB transposon


title: NTM_pt3 [S58_L001, S58_L002]


title: NTM_pt4 [S61_L001, S61_L002]


title: sp_2dpf_1a_scRNAseq

value: 2dpf gastrula

value: 2 dpf


title: nirB transposon replicate 3


title: NTM_pt3 [S59_L001, S59_L002]


title: ∆P11 sRNA deletion replicate 2

value: P11 sRNA deletion


title: nirB transposon replicate 1


title: NTM_pt3 [S56_L001, S56_L002]

value: Lung


title: sp_2dpf_3_scRNAseq


title: ∆P11 sRNA deletion replicate 1


title: sp_2dpf_2_scRNAseq


title: wildtype replicate 3

value: wildtype


title: ∆P11 sRNA deletion replicate 3


title: NTM_pt3 [S55_L001, S55_L002]


title: WAPLKO_A

value: B cells

value: WAPL KO


title: wildtype replicate 1


title: sp_2dpf_1_scRNAseq


title: NTM_pt3 [S54_L001, S54_L002]

value: wt


title: control_C

value: control


title: NTM_pt3 [S53_L001, S53_L002]

value: stromal cells


title: Visium, Irf3EC Day 3 MI (V55) biol rep2

city: La Jolla

first: Kevin

middle: Robert

last: King

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: UCSD

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software v6.1.1  or Space Ranger v1.3.1
Further processing was done with Seurat v4.3 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Highly variable gene markers were identified using SCTransform v2 from Seurat R package version 4.3
Assembly: refdata-gex-mm10-2020-A; refdata-gex-GRC38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Cardiac

extract_protocol:
Sections obtained from mice were imaged and processed for spatially resolved gene expression using the Visium Spatial Transcriptomics kit for Fresh/Frozen samples (10x Genomics). Samples were immediately snap-frozen in OCT using isopentane that was cooled in a liquid nitrogen bath. For cryosectioning, samples were equilibrated to −22 °C. 10 μm thick short axis sections were cut from the blocks onto Visium slides (10X Genomics) and processed according to the manufacturer’s protocol. Tissue permeabilization time was optimized at 30 minutes for infarcted mouse hearts. Hematoxylin and eosin (H&E) images generated during the Visium protocol were captured at 20x magnification on Nikon Eclipse Ti2-E widefield microscope and exported as tiled tiffs for analysis. Libraries were sequenced on the Illumina NovaSeq platform, and resulting data were processed using SpaceRanger (v.1.2.2, 10X Genomics)
Single-nucleus RNA-seq was performed by microfluidic droplet-based encapsulation, barcoding, and library preparation, (10X Genomics). Spatial transcriptomics assays were barcoded based on tissue-covered capture spot and library preparation was performed with 10X Genomics using dual-end indices. Paired end sequencing was performed on an Illumina Novaseq instrument. Low-level analysis, including demultiplexing, mapping to a reference transcriptome (mm10-2020-A or GRCh38-2020-A), and eliminating redundant UMIs, was performed with Cell Ranger 6.1.1 pipeline for 10X samples.

value: Cardiac

value: MI surgery


title: KOM-3

city: New Delhi

first: Dr. Meenu

last: Kapoor

address: Guru Gobind Singh Indraprastha University, Sector-16C, Dwarka

department: University School of Biotechnology (USBT)

country: India

data_processing:
BCL to Fastq conversion by bcl2fastq 2.19.0.316
The sequence data quality was checked using FastQC v0.11.9 and MultiQC v1.9 software. The data was checked for base call quality distribution, % bases above Q20, Q30, %GC, and sequencing adapter contamination. All the samples passed QC threshold (Q20>95%).
The sequence data was processed using fastp v0.20.1 to remove adapter sequences, low quality reads, filtering reads shorther than 50 bp.
The QC passed reads were mapped onto indexed Physcomitrium patens (assembly Phypa V3; GCA_000002425.2 [NCBI]) reference genome using STAR v2.7.8a aligner.
rRNA reads removed using bbmap’s bbduk algorithm.
Transcript assembly using StringTie
Gene level expression values were obtained as FPKM using cuffdiff v2.2.1
Genome_build: assembly Phypa V3; GCA_000002425.2
Supplementary_files_format_and_content: FPKM values in excel format

organism: Physcomitrium patens

source_name: Protonemata tissue

growth_protocol: 9 days on solid BCDAT medium + 5 days on liquid BCDAT medium

extract_protocol:
The RNA extraction was performed using TRIzol method.
Library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina.

treatment_protocol: 600 mM Mannitol stress for 24hour

value: Protonemata tissue

tag: ecotype

value: Gransden

tag: age

value: 14 day

value: 600 mM Mannitol stress for 24 hour


title: Visium, Irf3EC Day 3 MI (V52) biol rep1


title: NTM_pt3 [S52_L001, S52_L002]

value: nontuberculous mycobacterial lung disease

value: B lymphocyte


title: KOM-2

institute: Guru Gobind Singh Indraprastha University


title: Visium, Irf3Neut Day 3 MI (V56) biol rep2


title: Visium, Irf3Neut Day 3 MI (V49) biol rep1


title: Visium, Irf3Mac Day 3 MI (V58) biol rep2


title: NTM_pt3 [S51_L001, S51_L002]

value: T lymphocyte


title: NTM_pt3 [S50_L001, S50_L002]

value: macrophage


title: Visium, Irf3Mac Day 3 MI (V57) biol rep1


title: KOM-1


title: WT-M3

value: Wild type


title: wildtype replicate 2

value: bacteria

value: wildtype


title: Visium, Irf3FB Day 3 MI (V51) biol rep1


title: Visium, Irf3Cm Day 3 MI (V59) biol rep2


title: NTM_pt3 [S49_L001, S49_L002]

value: Lung


title: WT-M2


title: Visium, Ifnar-/- Day 3 MI (V54), biol rep2

value: Ifnar-/-


title: NTM_pt2 [S48_L001, S48_L002]

value: wt


title: WT-M1


title: NTM_pt2 [S47_L001, S47_L002]


title: Visium, Irf3Cm Day 3 MI (V50) biol rep1, Ruptured MI biol rep5


title: Visium, Ifnar-/- Day 3 MI (V53), biol rep1


title: Mature leaf, 50μM Pi

city: Perth

first: Patrick

middle: Michael

last: Finnegan

state: WA

address: 35 Stirling Hwy

department: School of Biological Sciences

country: Australia

institute: University of Western Australia

data_processing:
Reads with erroneous kmers were corrected using rCorrector (v1.0.4) and low-quality bases and adapters were trimmed with Trim-galore! (v0.6.6).
Trimmed reads were de novo assembled in Trinity (v2.12.0) and peptide sequences encoded by the assembled transcripts were predicted using TransDecoder (v5.5.0).
A reference transcriptome for expression quantification was generated by extracting transcripts corresponding to the peptide sequences in the peptide set.
RNA-seq libraries were aligned to reference transcripts through Trinity with the kallisto mapper.
Differential expression of transcripts among the leaf developmental stages was tested using DESeq2 (ver. 1.30.1).
Assembly: De novo assembled.
Supplementary files format and content: Tab-delimited text file includes raw counts of transcripts for each library.

organism: Hakea prostrata

source_name: Mature leaf

growth_protocol: Leaves were harvested from five naturally-occuring Hakea prostrata plants at the UWA Field Station, Shenton Park, Western Australia (31.9496 S, 115.7973 E).  Cluster roots, white roots, and mature leaves in different Pi treatments were grown in hydroponics.

extract_protocol:
Frozen ground-up powder (100 mg) was mixed with Tris-HCl, LiCl, EDTA, lithium dodecyl sulfate, dithiothreitol, polyvinylpyrrolidone, polyvinylpolypyrrolidone, followed by Fruit-mate (Takara Biotechnology). After several chloroform:isoamyl alcohol extractions, RNA was concentrated by isopropanol precipitation, followed by another precipitation of the resuspended RNA in LiCl. The RNA pellet was washed with LiCl followed by two washes with ethanol, air dried, and resuspended in RNase free water. After removal of contaminating DNA (RQ1 DNase; Promega Corporation), the three replicates with the highest quality for each leaf developmental stage were selected for library preparation and sequencing.
Libraries for RNA-Seq were prepared from 1 µg RNA according to the manufacturer’s instructions (TruSeq Stranded Total RNA Kit with Ribo-Zero Plant, Illumina)

treatment_protocol: No specific treatment applied, but a replicate was collected for each leaf stage from the five harvested plants. Different Pi treatments were supplied to white roots and mature leaves for plants in hydroponics, but no replicates were made.

value: Mature leaf

value: 50μM Pi


title: Mature leaf, 1μM Pi

value: 1μM Pi


title: Nmd5_24h_3

city: Kunming City, Yunnan Province

first: Liu

last: Qianqian

address: No.2 Cuihu North Road, Wuhua District

institute: Yunnan University

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The WT and ΔAonmd5 strains were cultured in a PDA medium for 7 days. Afterward, 200 C. elegans cells were added to each plate for 24 hours.

extract_protocol:
After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae


title: NTM_pt2 [S46_L002]


title: White root, 50μM Pi

source_name: White root

value: White root


title: Mature leaf, 10μM Pi

value: 10μM Pi


title: Nmd5_24h_2


title: NTM_pt2 [S45_L001, S45_L002]

value: stromal cells


title: White root, 10μM Pi


title: Nmd5_24h_1


title: NTM_pt2 [S44_L001, S44_L002]

value: nontuberculous mycobacterial lung disease


title: Nmd5_0h_3


title: Visium, Irf3FB Day 3 MI (V60) biol rep2

value: Cardiac

value: MI surgery


title: Cluster root, Day7

source_name: Cluster root

value: Cluster root


title: White root, 1μM Pi


title: Cluster root, Day4


title: NTM_pt2 [S43_L001, S43_L002]

value: T lymphocyte


title: Cluster root, Day1


title: NTM_pt2 [S42_L001, S42_L002]

value: macrophage


title: Nmd5_0h_2


title: Nmd5_0h_1

value: WT


title: Pig 26, huH1N1

city: Kongens Lyngby

first: Helena

last: Aagaard Laybourn

address: Søltofts Plads

country: Denmark

institute: Technical University of Denmark

data_processing:
The raw reads were filtered, which included adaptor removal, removal of contamination, and low-quality reads (ambiguous bases (N) higher than 5%, low-quality bases (quality score less than 10) higher than 20%, and having sequencing adaptor contamination).
Clean reads were mapped to the pig genome (Sscrofa11.1, NCBI accession: GCA_000003025.6) using HISAT2.
The clean reads were mapped to the transcript reference to quantify the gene expression using Bowtie2
RSEM was used to estimate the gene expression levels based on fragments per kilobase of exon per million fragments mapped (FPKM)
Data was normalized and differentially expressed genes were identified between different comparison groups by DESeq2
Assembly: Sscrofa11.1, NCBI accession: GCA_000003025.6
Supplementary files format and content: Excel file includes FPKM values for each sample

organism: Sus scrofa

source_name: Trachea

extract_protocol:
Whole sections of lower trachea were homogenized in QIAzol Lysis reagent (QIAGEN) using gentleMACS M tubes (Miltenyi Biotec). Total RNA was extracted using the miRNeasy mini kit (QIAGEN) and treated with an RNase-free DNase set (QIAGEN) according to the manufacturer’s instructions.
Libraries were constructed with a non-stranded and PolyA selection method according to the manufacturer’s specifications (BGI Genomics). Paired-end reads with a length of 100 bp were sequenced using the DNBSEQ platform.

value: Trachea


title: Pig 23, huH1N1


title: Pig 25, huH1N1


title: Cluster root, Day0


title: NTM_pt2 [S40_L001, S40_L002]

value: Lung

value: B lymphocyte


title: NTM_pt2 [S41_L001, S41_L002]

value: wt


title: AO_24h_3


title: NTM_pt2 [S39_L001, S39_L002]


title: Pig 24, huH1N1


title: Pig 21, huH1N1


title: AO_24h_1


title: Pig 22, huH1N1


title: AO_24h_2


title: AO_0h_3


title: Pig 12, swH1N1


title: Pig 13, swH1N1


title: Pig 19, huH1N1


title: NTM_pt1 [S35_L001, S35_L002]


title: Pig 11, swH1N1


title: Cluster root, Day12


title: NTM_pt2 [S38_L001, S38_L002]


title: Pig 14, swH1N1


title: NTM_pt1 [S36_L001, S36_L002]


title: Pig 20, huH1N1


title: AO_0h_1


title: AO_0h_2


title: ZR-75-1 fulvestrant-resistant cultured without fulvestrant

city: Lund

last: Persson

address: Scheelevagen 2

department: Dept of Clinical Sciences, Oncology

country: Sweden

institute: Lund University

data_processing:
Demultiplexed fastq files were generated by MiSeq Reporter v 2.6.2.3.
Adapter and base quality trimming were done with Cutadapt v 4.4 using the parameters -Q 30 -m 25 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Read alignment and methylation analysis were done with Bismark v 0.24.1 using Bowtie2.
Assembly: UCSC hg38
Supplementary files format and content: Tab-delimited text files with read counts per sample and CpG site for methylated or unmethylated bases, respectively.

growth_protocol: CAMA-1 and MCF7 cell lines were cultured in DMEM/F12 (Cytiva/HyClone), and EFM-19, HCC1428, T47D, and ZR-75-1 cell lines in RPMI-1640 (Cytiva/HyClone). All culture media were supplemented with 10% fetal bovine serum (Cytiva/HyClone) and cells were cultured at 37 °C, 5% CO2 in a humidified atmosphere. For maintenance, fulvestrant-resistant (FR) sublines were grown in complete medium supplemented with 100 nM fulvestrant.

extract_protocol:
DNA extraction was performed with the DNeasy Blood & Tissue kit (Qiagen) for 4 million cells per sample.
The EZ DNA Methylation-Lighting Kit (Zymo Research) was used for bisulfite conversion of 1 µg of genomic DNA per sample. PCR amplification of twelve 300-450 bp regions was done using KAPA HiFi HotStart Uracil ReadyMix Kit (Roche). PCR products were pooled per sample, resulting in 19 amplicon pools which were purified using the HighPrep PCR Clean-up System (MagBio Genomics Inc.) at a 1:1 ratio to remove fragments below 250 bp. The DNA concentration was determined using the Qubit dsDNA Broad Range Assay Kit (Invitrogen). The NEBNext Ultra II DNA Library Prep with beads and NEBNext Multiplex Oligos for Illumina (both from New England Biolabs) were used for preparation of sequencing libraries from 400 ng pooled and purified PCR products per sample. Library quality was evaluated using a Bioanalyzer with a High Sensitivity DNA chip (Agilent Technologies) and library concentration was determined with the Qubit dsDNA Broad Range Assay kit.

value: breast cancer cell line

tag: subline


title: ZR-75-1 fulvestrant-resistant

value: fulvestrant-resistant


title: Pig 10, swH1N1


title: Pig 9, swH1N1


title: ZR-75-1 parental cells

value: parental


title: NTM_pt1 [S32_L001, S32_L002]


title: NTM_pt2 [S37_L001, S37_L002]


title: Pig 8, swH1N1


title: NTM_pt1 [S33_L001, S33_L002]


title: NTM_pt1 [S34_L001, S34_L002]


title: T-47D fulvestrant-resistant cultured without fulvestrant


title: CTRL HiC rep2

data_processing:
Illumina HiSeq 2500 paired-end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605.1) using HiC-Pro v2.10.0 pipeline
Replicates per condition were merged and HiCcompare software was used to estimate significance of differential contact based on raw count matrix files. Samples were first normalized by library size and then by loess normalization. To determine filtering parameters the filter_params() function was used, applying numChanges = 1500, FC = 3 given the high resolution of the HiC matrices. A minimum average expression (A.min) was set to “15” and the p.method to “fdr” for the function hic_compare().
Only significantly changed associations (p-value < 5% and Z-score > 1 or < -1) were kept.
Interactions were plotted as circos graph using the circlize package (version 0.4.12) of R (version 4.0.5)
Assembly: NC_007605.1
Supplementary files format and content: Raw counts for each interactions
Supplementary files format and content: p- and q-value of interactions are provided in the matrix file

organism: human gammaherpesvirus 4

growth_protocol: Human MUTU I cells were cultured in RPMI (Life Technologies) with 10% FBS and 1% penicillan/streptomycin at 37 degrees C and 5% CO2.

extract_protocol:
Libraries of total ligation products were produced using Ultralow Library Systems V2 as per manufacturer’s protocol.
Purified libraries were then enriched for only EBV genome ligation products using myBaits enrichment kit as per manufacturer’s protocol.

treatment_protocol: 5 million cells per condition were collected for in-situ Hi-C as per Rao et al. Cell 2014.

value: MUTU I


title: CTRL HiC rep1


title: T-47D fulvestrant-resistant


title: NTM_pt1 [S31_L001, S31_L002]


title: WAPL KO HiC rep2


title: WAPL KO HiC rep1


title: Pig 7, swH1N1


title: bulkRNA_cMN7_Isl1-pos_E11-5B

first: Elizabeth

middle: C

last: Engle

address: 3 Blackfan Circle

institute: Boston Childrens Hospital

data_processing:
Basecalling performed Illumina HiSeq 2500 software
Generation of R1 and R2 reads for each of 2 lanes of data/sample that were subsequently concatenated
STAR (Spliced Transcripts Alignment to a Reference)134, a splice-aware tool, was used to align reads to ENSEMBL Mus musculus genomic reference build GRCm38.87
RSEM (RNA-Seq by Expectation Maximization)135 was used to generate the count files
DESeq2 was used to perform differential expression analysis
Assembly: mm10
Supplementary files format and content: Tab delimited .results files displaying transcript IDs and abundances

source_name: CN7 e11.5 GFP-positive

extract_protocol:
GFP positive and negative cells FACS purified from e10.5 or e11.5 cells
Standard Illumina chemistry

value: CN7 e11.5 GFP-positive

value: WILDTYPE


title: T-47D parental cells


title: Pig 6, control


title: MCF7 fulvestrant-resistant cultured without fulvestrant


title: Pig 5, control


title: NTM_pt1 [S30_L001, S30_L002]

value: nontuberculous mycobacterial lung disease


title: bulkRNA_cMN7_Isl1-pos_E10-5B

source_name: CN7 e10.5 GFP-positive

value: CN7 e10.5 GFP-positive


title: bulkRNA_cMN7_Isl1-pos_E11-5A


title: Pig 4, control


title: MCF7 fulvestrant-resistant


title: MCF7 parental cells


title: NTM_pt1 [S28_L001, S28_L002]


title: bulkRNA_cMN7_Isl1-pos_E10-5A


title: HCC1428 fulvestrant-resistant cultured without fulvestrant


title: Pig 3, control


title: bulkRNA_cMN6_Hb9-pos_E11-5B

source_name: CN6 e11.5 GFP-positive

value: CN6 e11.5 GFP-positive


title: Pig 2, control


title: HCC1428 fulvestrant-resistant


title: NTM_pt1 [S27_L001, S27_L002]

source_name: Lung


title: bulkRNA_cMN6_Hb9-pos_E11-5A2


title: Pig 1, control


title: HCC1428 parental cells


title: NTM_pt1 [S26_L001, S26_L002]


title: MYC_Twist1_OFF_3

city: Stanford

first: Renumathy

last: Dhanasekaran

address: 300 Pasteur Drive, Alway M211

institute: Stanford University

data_processing:
Trim adapters and low quality bases (Trimmomatic).
Align to the reference genome (STAR).
Determine the distribution of the bases within the transcripts and 5'/3' biases (Picard).
FPKM value was quantified by FeatureCounts tool
DESeq2 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Tumor tissue

extract_protocol:
Liver tumors were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy kit.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: organ

value: Liver

value: hepatocellular carcinoma

tag: group


title: BE_pt4 [S24_L001, S24_L002]

value: bronchiectasis

tag: cell type


title: bulkRNA_cMN4_Isl1-pos_E11-5B

source_name: CN4 e11.5 GFP-positive

value: CN4 e11.5 GFP-positive


title: EFM-19 fulvestrant-resistant cultured without fulvestrant


title: bulkRNA_cMN6_Hb9-pos_E11-5A1


title: NTM_pt1 [S25_L001, S25_L002]

tag: tissue

value: stromal cells


title: MYC_Twist1_OFF_2


title: BE_pt4 [S23_L001, S23_L002]

value: Lung

value: T lymphocyte


title: NTM_pt1 [S29_L001, S29_L002]

value: wt


title: bulkRNA_cMN4_Isl1-pos_E11-5A


title: MYC_Twist1_OFF_1


title: bulkRNA_cMN4_Isl1-pos_E10-5B

source_name: CN4 e10.5 GFP-positive

value: CN4 e10.5 GFP-positive


title: BE_pt4 [S22_L001, S22_L002]

value: macrophage


title: EFM-19 parental cells

tag: cell line

value: breast cancer cell line

value: parental


title: BE_pt4 [S21_L001, S21_L002]

tag: genotype


title: MYC_Recur_3


title: CAMA-1 fulvestrant-resistant cultured without fulvestrant week 17


title: CAMA-1 fulvestrant-resistant cultured without fulvestrant week 9


title: BE_pt3 [S20_L001, S20_L002]

value: B lymphocyte


title: MYC_Recur_1


title: CAMA-1 fulvestrant-resistant

value: fulvestrant-resistant


title: bulkRNA_cMN3_Isl1-pos_E11-5B

source_name: CN3 e11.5 GFP-positive

value: CN3 e11.5 GFP-positive

value: WILDTYPE


title: bulkRNA_cMN4_Isl1-pos_E10-5A


title: bulkRNA_cMN3_Isl1-pos_E11-5A


title: BE_pt3 [S19_L001, S19_L002]


title: MYC_OFF_3


title: EFM-19 fulvestrant-resistant


title: CAMA-1 parental cells


title: MYC_OFF_2


title: BE_pt3 [S18_L001, S18_L002]


title: bulkRNA_cMN3_Isl1-pos_E10-5B

source_name: CN3 e10.5 GFP-positive

value: CN3 e10.5 GFP-positive


title: BE_pt3 [S17_L001, S17_L002]


title: miRNA in the cultured neuron transfected with AAV-Gata1 [GT_small RNAseq]

first: Koeul

last: Choi

address: 84, Heukseok-ro

institute: Chung-Ang university

data_processing:
ChIPseq; Sequence reads were mapped to the mouse genome (mm9) using BWA. Peak calling was performed using HOMER findPeaks program, input DNA without ChIP as reference, with the default settings except for region size, which was 75, and minDist, which was 200. Peaks were annotated using HOMER annotatePeaks.pl tool.
RNAseq; Low quality reads containing more than 10% of skipped bases, more than 40% of bases whose quality scores are less than 20 and reads of which average quality scores of each read is less than 20 were filtered. Filtered reads were mapped to the mouse genome (mm10) using the aligner TopHat (v2.1.1). The data were assembled into transcripts by the Cufflinks (v2.1.1). Differential expression analysis was performed by Cuffdiff (v2.1.1). To enhance the analysis accuracy, multi-read correction and frag-bias-correct options were applied. All other options were set to default values. The P-values corrected through the Benjamini‒Hochberg method.
miRNAseq; After removing the sequencing adapters, quality control checks on raw reads were performed using Fast QC v0.11.5. Low-quality bases at the 3ʹ ends (<Q20) were trimmed and the reads shorter than 17 nucleotides were discarded. The remaining high-quality reads were mapped to the reference mouse genome (mm10) using Bowtie v1.1.2, with the following parameters: only 1 mismatch (-n 1), max 80 mismatch quals across alignment, 30 seed length, and the suppression of reads showing >5 alignments. The number of reads that mapped to each gene in each sample were counted using HTseq v0.6.1p1. Differentially expressed genes were identified based on the trimmed mean of M value (TMM) normalization method using edgeR v3.10.2 in R package, with the default parameters. The P-values were calculated using Fisher’s exact test and corrected through the Benjamini‒Hochberg method using the p.adjust function in R package.
Genome_build: mm9, mm10
Supplementary_files_format_and_content: bedgraph for ChIPseq samples, tab-delimited text files include FPKM of COUNT values for RNAseq and smallRNAseq samples

source_name: primary cortical neuron

extract_protocol:
Cultured cortical neurons (at DIV11) were cross-linked with 1% (v/v) formaldehyde, followed by adding 125mM of glycine to quench the cross-linking reaction. The cells were lysed in SDS lysis buffer including protease inhibitors and phosphatase inhibitors. Sheared chromatin was immunoprecipitated with Dynabead conjugated with 1ug of H3K4me3, H3K27me3 -specific antibodies or control IgG antibodies overnight at 4℃ with rotating. After reverse crosslinking, DNA was purified by using phenol-chloroform and ethanol precipitation. Total RNA extraction was performed using miRNeasy mini kit.
The ChIPed DNA was used for library preparation using NEBNext® UltraTM DNA library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s instructions. The ChIPed DNA was ligated with adaptors. After purification, PCR reaction was done with adaptor-ligated DNA and index primer for multiplexing sequencing. Library was purified by using magnetic beads. For mRNAseq, the libraries were prepared for 100bp paired-end sequencing using TruSeq Stranded mRNA library preparation kit (Illumina). The fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared. The cDNA libraries were amplified with PCR. Small RNA sequencing libraries were constructed using NEXTFLEX® Small RNA-seq Kit v3 for Illumina® Platform (PerkinElmer). The adapters are directly, and specifically, ligated to the microRNA molecules. The 5’ and 3’ NEXTFLEX adapter ligated products were reverse transcribed to create single stranded cDNA. The cDNA is then PCR amplified. The amplified cDNA constructs were separated on a 6% TBE gel and the 140-160bp bands were excised.

value: ICR

tag: tissue/age

value: cultured corticol neurons derived from E14 ICR mice at DIV11

tag: treatment


title: BE_pt3 [S16_L001, S16_L002]

value: bronchiectasis


title: bulkRNA_cMN3_Isl1-pos_E10-5A


title: MYC_OFF_1

value: Liver

value: hepatocellular carcinoma


title: Input_2

city: Riverside

first: feng

last: tang

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

data_processing:
Trim Galore was used to remove low-qualified bases and adapter-containing reads from raw spKAS-seq data. Duplicated reads were removed using Picard MarkDuplicates.
Trimmed reads were aligned to the human hg19 reference genome using Bowtie2 with the default configuration
Definitions of R-loops by spKAS-seq were performed by following previously reported procedures (PMID: 36449625)
Assembly: hg19
Supplementary files format and content: bed files were genereated using bedtools by merging the peaks of two replicates
Supplementary files format and content: bw files were generated using deeptools
Library strategy: Strand-specific kethoxal-assisted single-stranded DNA (ssDNA) sequencing (spKAS-seq)

source_name: HEK293T cells

growth_protocol: Cells were maintained in DMEM (Life Technologies) supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2. For genomic DNA extraction, the cells were harvested at 80% confluence. Cell lines used in this study were examined for a mycoplasma contamination test using e-Myco Mycoplasma PCR Detection Kit (Bulldog Bio. Inc.).

extract_protocol:
The purified genomic DNA was subsequently mixed with 5 μl of 20 mM dibenzocyclooctyne-PEG4-biotin conjugate (Sigma-Aldrich, 760749) and 10 μl of 10× phosphate-buffered saline (PBS), and the total volume was adjusted to 100 μl with 25 mM K3BO3. The resulting mixture was shaken gently at 37°C for 1.5 h, followed by addition of 5 μl of 10 mg/mL RNase A (Thermo Fisher Scientific, 12091039), and the mixture was shaken at 37°C for another 5 min. After the reaction, the DNA was isolated using the DNA Clean & Concentrator-5 kit (Zymo Research, D4013) and fragmented by sonication to 150 to 350 base pairs (bp). The sonicated DNA was employed for enrichment using 10 μl of Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific, 65001). The beads were washed with 1× binding and washing (B&W) buffer (5 mM tris-HCl, pH 7.4, 0.5 mM EDTA, 1 M NaCl, and 0.05% Tween 20), resuspended in 95 μl of 2× B&W buffer, and mixed with the sonicated DNA. The suspension was incubated at room temperature for 15 min. The beads were then washed once with 1× B&W buffer, twice with 100 mM NaOH solution to denature the dsDNA and remove the DNA strands that are not labeled by N3-kethoxal, and once again with 1× B&W buffer. The DNA was eluted from the beads by heating the beads in 10 μl H2O at 95°C for 10 min.
The ensuing enriched DNA and the corresponding input were employed for library construction using the Accel-NGS Methyl-Seq DNA Library Kit (Swift, 30024) following the manufacturer’s instructions. Subsequently, the purified DNA libraries were assessed using an Agilent 2100 Bioanalyzer and multiplexed for sequencing on a MGISEQ-2000 platform (BGI).

treatment_protocol: spKAS-seq was conduceted following previously published procedures with minor modifications (PMID: 36449625), where N2-heptynyl-dG was added to the culture medium until its final concentration reached 10 μM. After a 3-h incubation, the cells were treated with 5 mM N3-kethoxal dissolved in the culture medium for 10 min at 37°C, then harvested for genomic DNA isolation using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific, K182002).

value: HEK293T cells

value: Human embryonic kidney

value: WT


title: Input_1


title: MYC_Recur_2


title: miRNA in the cultured neuron transfected with AAV-Control [CT_small RNAseq]

city: Seoul

tag: strain

value: AAV-Control


title: KN99a CR 2

city: Stony Brook

first: Natalia

last: Kronbauer de Oliveira

state: NY

address: 100 Nicolls Rd

institute: Stony Brook University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GCcontent the clean data were calculated.
Assembly: Clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: Raw data were processed by removing reads containing adapters, reads containing unknown nucleotides, and low-quality reads. Differential expression analysis was performed employing the DESeq2 R package. Genes with an adjusted p-value ≤ 0.05 and |log2FoldChange| ≥ 0.5 were assigned as differentially expressed.

organism: Cryptococcus neoformans

growth_protocol: Cells were grown overnight in synthetic media (SM): 1.7 g yeast nitrogen base without amino acids,1 g Drop-Out mix, 0.4% ethanol, 5 g (NH4)2SO4, 3.3 g NaCl, with 2% glucose per 1L; or calorie restriction media (CR): 1.7 g yeast nitrogen base without amino acids,1 g Drop-Out mix, 0.4% ethanol, 5 g (NH4)2SO4, 3.3 g NaCl, with 0.05% glucose per 1L

extract_protocol:
RNA was extracted using the QIAGEN RNAeasy Plus kit
RNASeq was performed by Novogene Co. Libraries were clustered and sequenced on an Illumina NovaSeq 6000 platform, which utilizes a paired-end 150bp sequencing strategy according to the manufacturer's instructions.

treatment_protocol: Cells were washed twice with 1x PBS

value: 0.05% glucose calorie restriction media


title: BE_pt3 [S15_L001, S15_L002]

data_processing:
Library strategy: Spatial Trtanscriptomics
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads
Sequencing reads were mapped to the hg38 human using STAR v2.7.3a
Gene level abundance was quantitated from the filtered human alignments in R using the GenomicAlignments Bioconductor package (version 1.22.1)
Assembly: hg38
Supplementary files format and content: digital count conversion (.dcc) file

extract_protocol:
RNA extracted by column purification using an RNA isolation kit Rneasy (Qiagen) according to the manufacturer's protocol
RNAseq libraries were constructed from 1ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit

value: Lung

value: T lymphocyte

value: wt


title: MYC_Twist1_HCC_5 (re-analyzed)

description: re-analysis of GSM4037029


title: MYC_Twist1_HCC_4 (re-analyzed)

description: re-analysis of GSM4037028


title: BE_pt3 [S13_L001, S13_L002]

value: stromal cells


title: KN99a SM 2

value: 2% glucose synthetic media


title: KN99a SM 1


title: KN99alpha CR 2


title: BE_pt3 [S14_L001, S14_L002]

value: macrophage


title: no IP DNA after infection with AAV-Gata1 [GT_input DNA]


title: KN99a CR 1


title: BE_pt2 [S9_L001, S9_L002]


title: Total RNA in the cultured neuron transfected with AAV-Gata1 [GT_RNAseq]


title: BE_pt2 [S12_L001, S12_L002]

value: B lymphocyte


title: KN99alpha SM 2


title: MYC_Twist1_HCC_2 (re-analyzed)

description: re-analysis of GSM4037026


title: BE_pt2 [S11_L001, S11_L002]


title: Total RNA in the cultured neuron transfected with AAV-Control [CT_RNAseq]

value: ICR


title: MYC_Twist1_HCC_3 (re-analyzed)

description: re-analysis of GSM4037027


title: BE_pt2 [S10_L001, S10_L002]


title: DNA immunoprecipitated with H3K4me3 antibodies after infection with AAV-Gata1 [GT_H3K4me3_ChIPseq]

value: cultured corticol neurons derived from E14 ICR mice at DIV11

tag: chip antibody

value: anti-Histone H3 (tri methyl K4) antibody (Abcam, ab8580, GR240214-3)


title: DNA immunoprecipitated with H3K27me3 antibodies after infection with AAV-Control [CT_H3K27me3_ChIPseq]

value: anti-trimethyl-Histone H3 (Lys27) antibody (Merck Millipore, 07-449, 2686928)


title: MYC_HCC_5 (re-analyzed)

description: re-analysis of GSM4037024

value: Liver

value: hepatocellular carcinoma


title: no IP DNA after infection with AAV-Control [CT_input DNA]


title: BE_pt1 [S8_L001, S8_L002]

value: bronchiectasis


title: DNA immunoprecipitated with H3K27me3 antibodies after infection with AAV-Gata1 [GT_H3K27me3_ChIPseq]


title: KN99alpha CR 1


title: MYC_Twist1_HCC_1 (re-analyzed)

description: re-analysis of GSM4037025


title: BE_pt1 [S7_L001, S7_L002]


title: MYC_HCC_1 (re-analyzed)

description: re-analysis of GSM4037020


title: Wild leaf, Stage M, rep 3

source_name: Wild leaf

value: Wild leaf

value: Stage M


title: MYC_HCC_2 (re-analyzed)

description: re-analysis of GSM4037021


title: MYC_HCC_4 (re-analyzed)

description: re-analysis of GSM4037023


title: Wild leaf, Stage M, rep 2


title: BE_pt1 [S5_L001, S5_L002]


title: Wild leaf, Stage M, rep 1


title: Islet ob/ob rep4

city: Hangzhou

first: Meng

last: zhuoxian

state: Zhejiang

address: 866 Yuhangtang Road, Xihu District

department: Department of Pathology and Pathophysiology

institute: Zhejiang University School of Medicine

data_processing:
The raw reads were filtered and trimmed with SOAPnuke (V1.4.0) and trimmomatic (V0.36)
Filtered clean data were then aligned to mm10 reference genome (Mus_musculus.GRCm38.90) with HISAT214 (V2.1.0)
Expression level of mRNA statistical analysis performed with Deseq2 (v.1.20.0) package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreatic islet

extract_protocol:
Mouse islets were isolated from pancreas by intraductal collagenase (Collagenase Type V, 1 mg/ml, Sigma, C9263) digestion, and purified by Histopaque 1077 (Sigma, 10771) density gradient centrifugation, and hand-picked under stereo microscope.RNA was harvested using Trizol reagent and a phenol-chloroform extraction was performed to isolate RNA. 1 ug of total RNA for the construction of sequencing libraries.
Library construction, and sequencing were performed by Beijing Genomic Institution (www.genomics.org.cn, BGI) using an optimized data analysis workflow.

value: Pancreatic islet

value: 12 weeks

value: ob/ob


title: KN99alpha SM 1


title: MYC_HCC_3 (re-analyzed)

description: re-analysis of GSM4037022


title: BE_pt1 [S6_L001, S6_L002]

value: Lung

value: wt


title: Delta-TRRAP_RNAseq_Rep2

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description: Delta-TRRAP EP400, rep2

data_processing:
Reads aligned with STAR RNA-Seq aligner (version 2.7.10b) with the following options: --outSJfilterReads Unique --outFilterMultimapNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif.
STAR output .sam files converted to .bam files with samtools2 (version 1.15.1)
.bam files sorted by name (-n) with samtools2 (version 1.15.1)
Reads overlapping annotated genes (GENECODE v32 annotations) counted with HTSeq (version 2.0.2) with the following options: htseq-count --stranded=reverse –order=name -f bam --additional-attr=gene_name -m union.
HTSeq output raw counts used to find differentially expressed genes with DESeq2, run with default parameters within the Galaxy platform5 (DESeq2 Galaxy Version 2.11.40.8+galaxy0)
bigWig coverage files generated with deepTools bamCoverage (version 3.5.1) with the following options: --binSize 50 --normalizeUsing BPM
Assembly: hg38
Supplementary files format and content: Normalized_counts_stranded.tabular: single table containing the DESeq2 output of normalized transcripts counts for each replicate of each condition
Supplementary files format and content: WT_vs_HSA_6mut_stranded.tabular: table containing the result of DESeq2 differential gene expression analysis comparing WT and HSA-6mut EPC1 replicates; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj
Supplementary files format and content: WT_vs_Delta_TRRAP_stranded.tabular: table containing the result of DESeq2 differential gene expression analysis comparing WT and Delta-TRRAP EPC1 replicates; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj
Supplementary files format and content: *.bw files: coverage files generated with deepTools
Supplementary files format and content: *htseqCounts.txt: raw transcripts counts for each condition and replicate; HTSeq output.

growth_protocol: RPMI medium 1640 1x, 5% Newborn Calf Serum (Thermo Fisher Scientific 16010159), 1% GlutaMAX

extract_protocol:
Monarch Total RNA Miniprep Kit (NEB T2010S), according to manufacturer’s instructions
mRNA enrichment with NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L), then library construction with KAPA RNA HyperPrep (Roche, 08098107702) according to manufacturers' instructions

treatment_protocol: 500 nM dTAGV-1 for 24h

value: Lymphoblast

value: endogenous EP400-dTAG + exogenous Delta-TRRAP EP400


title: Wild leaf, Stage 4, rep 3

value: Stage 4


title: BE_pt1 [S4_L001, S4_L002]

last: Koh

address: Jongnogu 101 Seoul National University hospital, B1, Department of Pathology

institute: Seoul National University Hospital

value: B lymphocyte


title: BE_pt1 [S3_L001, S3_L002]

value: T lymphocyte


title: Islet ob/ob rep3


title: Wild leaf, Stage 4, rep 2


title: WT_RNAseq_Rep3

description: WT EP400, rep3

value: endogenous EP400-dTAG + exogenous WT EP400


title: Delta-TRRAP_RNAseq_Rep1

description: Delta-TRRAP EP400, rep1


title: BE_pt1 [S2_L001, S2_L002]

value: macrophage


title: Islet ob/+ rep4

value: ob/+


title: WT_RNAseq_Rep2

description: WT EP400, rep2


title: Wild leaf, Stage 4, rep 1


title: Islet ob/ob rep1


title: Islet ob/ob rep2


title: DNA immunoprecipitated with H3K4me3 antibodies after infection with AAV-Control [CT_H3K4me3_ChIPseq]

value: ICR

value: cultured corticol neurons derived from E14 ICR mice at DIV11

value: AAV-Control

value: anti-Histone H3 (tri methyl K4) antibody (Abcam, ab8580, GR240214-3)


title: Delta-TRRAP_RNAseq_Rep3

description: Delta-TRRAP EP400, rep3


title: MGH314_organoid_scRNA

first: Jingyi

last: Wu

address: 360 Longwood Ave

department: Department of Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
Fastqs were aligned to hg38 genome using STARsolo. The following STARsolo parameters were used: --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13 --soloUMIlen 8 --outSAMtype BAM SortedByCoordinate --outSAMattributes CR UR CY UY CB UB. The raw matrices outputs of STARsolo for each library were gzipped and used as input for Seurat by utilizing the Read10X() function with the default parameters.
processed data files format and content: gene_expression_matrix
Assembly: hg38

source_name: patient-derived organoid

growth_protocol: The primary tumor pieces right out of the operating room were distributed in 6-well culture plates with 4 mL of the organoid medium as previously described and placed on an orbital shaker rotating at 120 rpm within a 37C, 5% CO2, and 90% humidity sterile incubator. The medium was changed every other day by tilting the plates without disturbing the organoid. The tumor pieces generally formed rounded organoids within 2 weeks.

extract_protocol:
Cells are lysed with a lysis buffer and mRNA binds to the polyT sequence on the oligo that is linked to the bead.
Seq-Well was performed with 18 PCR cycles for WTA, and a template switching oligo with an LNA-modification of the last guanine.

treatment_protocol: After 2-3 weeks of maturation of the organoids, the 4 ul of DNMT1 inhibitor (GSK3484862) and DMSO were added to the medium to make a final concentration of 1uM of DNMT1 inhibitor.

value: patient-derived organoid

value: DNMT1 inhibitor


title: WT_RNAseq_Rep1

description: WT EP400, rep1


title: BE_pt1 [S1_L001, S1_L002]

first: Jaemoon

value: bronchiectasis

value: stromal cells


title: Wild leaf, Stage 3, rep 2

value: Wild leaf

value: Stage 3


title: Placenta_8 [Nromal 5]

city: Wuhan

first: Mi

address: Tongji Medical College, No. 13 Hangzhou Road, Qiaokou District, Wuhan

department: Immunology

institute: 华中科技大学

data_processing:
Illumina HiSeq platform used for basecalling.
Raw image Data files obtained by Illumina HiSeq are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fq) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with RPKM values for every gene and every sample

source_name: placenta

extract_protocol:
Total RNAs were extracted from cells using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta

value: Normal


title: Islet ob/+ rep3

value: Pancreatic islet

value: 12 weeks


title: Islet ob/+ rep2


title: Placenta_7 [Nromal 4]


title: MGH240_organoid_scRNA


title: Wild leaf, Stage 3, rep 3


title: Islet ob/+ rep1


title: Wild leaf, Stage 3, rep 1


title: Placenta_6 [PTB 3]

value: PTB


title: BWH14_primary_scRNA

source_name: primary tissue

value: primary tissue

value: no


title: Wild leaf, Stage 2, rep 2

value: Stage 2


title: Placenta_5 [Nromal 3]


title: Wild leaf, Stage 2, rep 1


title: Placenta_4 [PTB 2]


title: Placenta_3 [Nromal 2]


title: BWH14_scATAC

data_processing:
CellRanger ATAC (version 1.1.0) was used for alignment, deduplication, and generating the single cell matrix, using GRCh38 as a reference.
processed data files format and content: filter_peak_matrix
processed data files format and content: single_cell_metadata
Assembly: hg38

extract_protocol:
Nuclei were spun down and resuspended in 100 ul of lysis buffer for 4 min on ice. Nuclei were washed with 200-400 ul wash buffer and counted with trypan blue staining, then resuspended with sufficient nuclei buffer to achieve a concentration of 2000 nuclei/ul.
To perform tagmentation, 5 ul of nuclei suspension was added to 7 ul of ATAC buffer (10X Genomics) and 3 ul of Tn5 and incubated at 37°C for 1 h. Nuclei capture and library prep was then performed according to the 10X Genomics scATAC-seq protocol.


title: Wild leaf, Stage 1, rep 3

value: Stage 1


title: BWH3_scATAC


title: MGH240_scATAC


title: Placenta_2 [PTB 1]


title: Placenta_1 [Nromal 1]


title: Wild leaf, Stage 1, rep 1


title: MGH239_scATAC


title: Aldh2-/-Sptbn1+/-, replicate 5, RNAseq

city: Manhasset

first: Lopa

last: Mishra

address: 350 Community Drive

institute: The Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: hg38 for human samples; mm10 for mice samples
Supplementary files format and content: tab-delimited text files include fpkm values for each sample from mice; TPM values for each sample from human MASH model

source_name: liver

extract_protocol:
For RNA-seq, RNA was extracted from liver tissues and the MASH model cells using the RNeasy Plus Mini kit. RNA quality and concentration were assessed using the Thermo Scientific Nanodrop spectrophotometer before RNA sequencing.
About 1 μg of RNA was used to generate barcoded sequencing libraries. Novogene Corporation performed library preparation.

value: liver cells

value: liver


title: Wild leaf, Stage 1, rep 2

data_processing:
Reads with erroneous kmers were corrected using rCorrector (v1.0.4) and low-quality bases and adapters were trimmed with Trim-galore! (v0.6.6).
Trimmed reads were de novo assembled in Trinity (v2.12.0) and peptide sequences encoded by the assembled transcripts were predicted using TransDecoder (v5.5.0).
A reference transcriptome for expression quantification was generated by extracting transcripts corresponding to the peptide sequences in the peptide set.
RNA-seq libraries were aligned to reference transcripts through Trinity with the kallisto mapper.
Differential expression of transcripts among the leaf developmental stages was tested using DESeq2 (ver. 1.30.1).
Assembly: De novo assembled.
Supplementary files format and content: Tab-delimited text file includes raw counts of transcripts for each library.

extract_protocol:
Frozen ground-up powder (100 mg) was mixed with Tris-HCl, LiCl, EDTA, lithium dodecyl sulfate, dithiothreitol, polyvinylpyrrolidone, polyvinylpolypyrrolidone, followed by Fruit-mate (Takara Biotechnology). After several chloroform:isoamyl alcohol extractions, RNA was concentrated by isopropanol precipitation, followed by another precipitation of the resuspended RNA in LiCl. The RNA pellet was washed with LiCl followed by two washes with ethanol, air dried, and resuspended in RNase free water. After removal of contaminating DNA (RQ1 DNase; Promega Corporation), the three replicates with the highest quality for each leaf developmental stage were selected for library preparation and sequencing.
Libraries for RNA-Seq were prepared from 1 µg RNA according to the manufacturer’s instructions (TruSeq Stranded Total RNA Kit with Ribo-Zero Plant, Illumina)


title: HLM140_2, scRNAseq of 1 sample

city: Hannover

first: Sarina

last: Ravens

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: 10x Genomics

data_processing:
The scRNAseq libraries were sequenced on the NovaSeq X platform, targeting 25,000 read pairs per cell. Reads were aligned to the reference genome GRCh38, and the gene expression matrix was generated using Cell Ranger 7.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: gene expression matrix

source_name: untreated PBMC

extract_protocol:
The PBMCs were thawed and fluorescence-activated cell sorting (FACS) was performed to isolate live CD3+TCRαβ-TCRγδ+ cells and live CD3+TCRαβ+TCRγδ- cells.
These sorted T cells were then used to generate single-cell RNA sequencing (scRNAseq) libraries with the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (for infants) and v2 (for 5-11-year-old children), following the manufacturer’s protocol (10x Genomics).

tag: disease condition

value: Congenital heart disease

value: day 189

tag: sampling time

value: 6 month after cardiac surgery

value: untreated

value: PBMC


title: Aldh2-/-Sptbn1+/-, replicate 3, RNAseq


title: MGH240_primary_scRNA

city: Boston


title: NC4CD4TRM

city: Changsha

first: zhidan

last: zhao

address: #139 Renmin Middle Road, The 2nd Xiangya Hospital

institute: central south university

data_processing:
The FASTQ files were processed in order to remove reads of zero length (fastq_trimmer v.1.0.0), remove adapter sequences (fastqmcf tool v.1.1.2) and perform quality trimming from both ends until a minimum base quality ≥ 30 (FASTQ quality trimmer tool v.1.0.0).
Reads were aligned to the human reference genome (build hg38) with TopHat (v.1.4.0) and read counts per Ensembl gene ID were quantified with htseq-count (v.0.4.1).
Quality metrics for the FASTQ and BAM/SAM files were generated with FastQC (v.0.11.3) and Picard (v.1.128).
Processing of FASTQ and BAM/SAM files was executed on the Galaxy workflow platform of Globus Genomics.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: CD4+ Trm cells

growth_protocol: The epidermis and dermis of skin samples from 3 ACLE patients and 3 healthy controls were separated by overnight incubation with dispase II (1.4 IU/ml, Roche Diagnostics) at 4°C. The dermis was minced and incubated with 1 mg/ml collagenase type IV (Worthington) for 1 h with vortexing every 20 min. The cell suspension was filtered through a 40-μm cell strainer and washed with PBS containing 2% FBS before staining. Cells were labeled with anti-CD4 PE-conjugated (BD Biosciences), anti-CD69 FITC-conjugated (BD Biosciences), and anti-CD103 APC-conjugated (BD Biosciences) antibodies and sorted using a BD Influx™ (BD Biosciences).

extract_protocol:
CD4+ Trm cells were sorted into lysis buffer using a BD FACSAria III (BD Biosciences) as much as possible
cDNA was generated by using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara),Library construction was performed using the NexteraXT DNA sample preparation kit (Illumina) using half the recommended volumes and reagents. Dual-index, single-read sequencing of pooled libraries was run on a HiSeq2500 sequencer (Illumina) with 58-base reads and a target depth of 5 million reads per sample. Base-calling and demultiplexing were performed automatically on BaseSpace (Illumina) to generate FASTQ files.

value: Skin

tag: disease state

value: NC


title: Aldh2-/-Sptbn1+/-, replicate 4, RNAseq


title: Wild leaf, Stage 2, rep 3

address: 35 Stirling Hwy

institute: University of Western Australia

value: Wild leaf


title: HLM140_1, scRNAseq of 1 sample

description: 10x Genomics

value: day 9

value: Before cardiac surgery


title: SLE4CD4TRM

value: SLE


title: MGH234_scATAC

value: primary tissue


title: Aldh2-/-Sptbn1+/-, replicate 2, RNAseq


title: HLM139_2, scRNAseq of 1 sample

description: 10x Genomics

value: day 188


title: MCF10CA1_LA_rep3

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation

data_processing:
Reads were mapped to the hg38 genome with Bowtie2 v2.4.1.
Mapped reads were used to call LaminB1 peaks (LADs) using 10 runs of Enriched Domain Detector with auto-estimation of GapPenalty and BinSize parameters, and mean GapPenalty and BinSize outputs from these runs were used for a final EDD run.
Assembly: hg38

source_name: Mammary tissue

growth_protocol: MCF10A, MCF10AT1, and MCF10Ca1a cell lines were grown in DMEM/Nutrient F12 (DMEM/F12) media supplemented with 5% horse serum (MCF10A and MCF10Ca1a) or 2.5% horse serum (MCF10AT1), 14 mM NaHCO3, 10 µg/mL insulin, 2 mM L-glutamine, 20 ng/mL human epidermal growth factor, 500 ng/mL Hydrocortisone and 100 ng/mL cholera Toxin. MCF10A cells were obtained from the American Type Culture Collection (CRL-10317). MCF10AT1 and MCF10Ca1a cells were obtained from the Barbara Ann Karmanos Cancer Institute (Detroit, Michigan).

extract_protocol:
For ChIP, cells were cross-linked for 10 min with 1% formaldehyde, sonicated in a Diagenode Bioruptor to produce chromatin fragments of ~200 base-pairs; lysates were clarified by sedimentation and Lamin B1-DNA complexes were isolated from supernatants by ChIP using antibodies against lamin B1, washed and DNA was eluted for library preparation. For input samples, cells were crossed, sonicated and lysaates clarified as above, and DNA was purified.
Diagenode Microplex library prepareation kit v2. TruSeq LT indexes, non-pooled samples.

treatment_protocol: All three cell types were cultured under proliferating conditions in media described above.

value: Mammary tissue

value: MCF10AC1 cell line

value: Mammary epithelium; xenograft derivative of MCF10A

value: Human, female

value: Culrured, adherent, transformed, malignant

tag: antibody

value: Anti-lamin B1, Abcam, ab16048


title: Aldh2-/-Sptbn1+/-, replicate 1, RNAseq

value: liver cells

value: liver


title: MGH232_scATAC

value: no


title: MCF10CA1_input_2

description: Formaldehyde crosslinking, DNA purification (PCI) and Illumina library preparation


title: HLM139_1, scRNAseq of 1 sample

description: 10x Genomics

value: Congenital heart disease

value: day 8

value: untreated

value: PBMC


title: MGH231_scATAC


title: Aldh2-/-, replicate 4, RNAseq


title: Aldh2-/-, replicate 3, RNAseq


title: HDF2_Lamin_WT

city: Epalinges

first: Soumitra

last: Ghosh

state: Choose State/Province

address: Chemin des Boveresses 155

department: Biochemistry

country: Switzerland

institute: University of Lausanne, Switzerland

description: HDFs expressing S301D lamin A/C

hyb_protocol: Libraries were hybridized to the human Clariom™ D arrays (Thermo Fisher Scientific).

scan_protocol: Standard Affymetrix protocol

data_processing: Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) was used for data processing and analysis.

source_name: Human Skin derived fibroblasts

label_protocol: The GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, Cat. No. 902280) was used to prepare samples and to facilitate hybridization to the human Clariom™ D arrays (Thermo Fisher Scientific).

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA extraction and purification was carried out using the Direct-zol RNA Miniprep Kit (Zymo Research)
The quality of RNA samples was assessed, ensuring a purity of OD260/OD280 ≥ 1.8 and RIN ≥ 8. Global transcriptomic analysis was conducted at the Institute of Genetics and Genomics of Geneva (iGE3) using Clariom™ D GeneChip assays.

treatment_protocol: HDF cells were transduced with either Phospho Ser 301 mimetic mutant (S301D) and WT lamin A/C expressing lentiviruses and selected with puromycin. 6 Days post-transduction, cells were harvested, total RNA was isolated.

value: HDF

value: S301D lamin A/C


title: MGH236_scATAC

value: primary tissue


title: HDF1_Lamin_WT

description: HDFs expressing S301D lamin A/C


title: HDF2_Lamin_S301D

description: HDFs expressing Wildtype lamin A/C

value: Wildtype lamin A/C