title: E8.75_rep2 [ATAC-Seq]

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: Wildtype E8.75 embryos

library_source: genomic single cell

data_processing:
FastQ files were processed using CellRanger arc version 2.0.0 using defult arguments
RNA: Reads were mapped to the mm10 genome and counted with GRCm38.92 annotation. Low-quality cells were filtered based on the distribution of QC metrics. Cells were required to have a minimum of 2000 UMIs per cell, a maximum of 40% mitochondrial reads and a maximum of 20% ribosomal reads. The resulting count matrix was stored using a SingleCellExperiment (Amezquita et al., 2019)  (v 1.14.1) object. Normalisation and log transformation was performed using scran(Lun et al., 2016) (v1.20.1) and scuttle (McCarthy et al., 2017)(v1.2.1). Doublet detection was performed using the hybrid approach in the scds (v1.8.0) package.
ATAC: We used the ArchR package (Granja et al., 2021)(v1.0.1) for preprocessing of ATAC data.  Briefly, arrow files were created from the ATAC fragment files. Cells were required to have a minimum of 3500 fragments per cell, a minimum TSS enrichment of 9, and a maximum blacklist ratio of 0.05. Pseudo-bulk replicates were obtained per cell type and peak calling was performed using macs2(Zhang et al., 2008) (v2.2.7.1) using the cell type identified from the RNA expression as a group. A consensus peak set was obtained by an iterative overlapping strategy which is better at preserving cell type-specific peaks. Motif annotations were extracted from the CISBP (Weirauch et al., 2014)  (v2) and JASPAR 2000 database (Castro-Mondragon et al., 2021). Motif matches for each peak were obtained using motifmatchr  (v1.14.1), with a minimum motif width of 7 and a maximum q-value of 1e-4. Bigwig files were exported for each cell type for visualisation on the IGV browser (J. T. Robinson et al., 2011) (v2.11.0).
Assembly: GRCm38
Supplementary files format and content: 10X GEX barcode file Tsv files contain barcodes of detected cells.
Supplementary files format and content: 10X GEX feature file Tsv files contain IDs of detected genes.
Supplementary files format and content: 10X GEX matrix file Mtx files contain matrix of raw count values.
Supplementary files format and content: 10X ATAC fragment file Tsv file of <chromosome><start><end><barcode><reads>
Supplementary files format and content: bigwig file bigwig files contain celltype specific ATAC-seq counts
Supplementary files format and content: ATAC peaks file ATAC peaks file contains the genomic locations of peaks and the celltype from which the peaks are called from
Supplementary files format and content: cell metadata file Cell metadata file contains statistics and sample information for each cell
Supplementary files format and content: celltype ATAC-seq peak matrix celltype ATAC-seq peak matrix contains pseudobulked ATAC-seq counts quantified in peaks for each celltype

source_name: Embryo

extract_protocol:
10x Genomics Single Multiome
10x Genomics Single Multiome
Following dissection, embryos from the same stages were pooled to give sufficient cell numbers. Embryos were dissociated into single-cells using 200μl of TriplE Express for 10 minutes at 37°C on a shaking incubator. 1ml of ice-cold 10% FBS in PBS was added to quench and cells were filtered using a 40μM Flowmi cell strainer. Following centrifugation at 300g for 5 minutes, the supernatant was discarded and cells were resuspended in 50μl of PBS containing 0.04% BSA. Cells were counted and viability assessed using trypan blue staining on a Countess II instrument (Invitrogen). >95% of cells were negative for trypan blue indicating high sample quality.     Nuclear isolation was carried out according to the low-cell input version of the 10X protocol for cell lines and PBMCs (https://assets.ctfassets.net/an68im79xiti/6t5iwATCRaHB4VWOJm2Vgc/bdfd23cdc1d0a321487c8b231a448103/CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB.pdf). Specifically, the 50μl cell suspension was transferred to a 0.2ml PCR tube and centrifuged at 300g for 5 minutes. After removing the supernatant, cells were resuspended in 50μl ice cold nuclear extraction (NE) buffer (10mM Tris pH 7.5, 10mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Tween, 1mM DTT, 1U/ul RNaseIn (Promega), 0.1% NP40, 0.01% Digitonin) and incubated on ice for 4 minutes. 50μl of wash buffer (identical to NE buffer but lacking NP40 and digitonin) was added and nuclei were centrifuged at 500g for 5 minutes at 4°C. After removing the supernatant, nuclei were washed once in 50μl of diluted nuclei buffer (10x Genomics), span down and finally resuspended in 7ul of dilute nuclei buffer (10x Genomics). 1μl was used to assess quality using a microscope and count nuclei using a Countess II instrument. >99% of nuclei stained positive for trypan blue and the nuclei were found to have the expected morphology. Nuclei were diluted such that a maximum of 16,000 were taken forward for 10x Multiome library preparation.
Libraries were prepared using the 10x Genomics Chromium
Combined snRNA-seq and snATAC-seq using 10x Genomics Multiome

value: Wildtype

tag: background


title: L3_control_ovaries_rep1

status: Public on Jun 16 2022

type: SRA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LCDB

country: USA

institute: NIDDK, NIH

description:
Pool of 25 ovaries with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.
Drosophila melanogaster (7227)
A1_OCP_1

library_source: transcriptomic

data_processing:
We processed the data by using a RNA-Seq work flow that is developed by LCDB core (https://github.com/lcdb/lcdb-wf). Briefly we de-multiplexd and convert BCL to FASTQ format. We removed the adaptors using Cutadapt. We created a reference using Flybase 6.32 and aligned reads with Hisat2 using default setting. We generated both transcript level counts and featureCounts using Salmon and featureCounts.
Assembly: Flybase 6.32
Supplementary files format and content: FeatureCount

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: We followed the Growth protocol as published in GSE115478. Briefly, we grew all the flies on Fly food A (LabExpress Ann Arbor, MI) in constant light at 25°C and 60% relative humidity. We collected eggs every 8-16 hr. from six mated females and allowed larvae to develop until the late third instar larval stage. For precise larval staging, we fed second and third instar larvae with water/yeast paste containing 0.5 mg/ml Sulforhodamine B sodium salt (Sigma-Aldrich, Cat. No. S1402-25G. St. Louis, MO). We selected larvae with mostly cleared foreguts that were immobilized, but that had no extended anterior spiracles.

extract_protocol:
We followed the Extraction Protocol from GSE115478. Briefly, we dissected larvae in 1XPBS at 22°C (Gibco Life Technologies, Carlsbad, CA) and separated the fatbody from the gonads. In order to separate the fatbody, we treated the gonads with 0.075 mg/ml Papain (Sigma-Aldrich, St. Louis, MO) and 0.075 mg/ml Collagenase enzyme (Sigma-Aldrich, St. Louis, MO) mixed in PBS in a 1.5ml Eppendorf tube for 3 min with gentle vertexing by flicking the tube with a forefinger. We washed the gonads twice with 1X PBS after decanting the floating fatbody cells. We collected each sample in a 350 μl RLT buffer (Qiagen, Cat. No. 79216. Valencia, CA), vortexed two times for 30 sec with a 30 sec interval and quickly frozen in a dry ice ethanol bath and stored at -80°C until RNA extraction. Using the RNeasy 96 kit, we extracted total RNA (Qiagen, Cat. No. 1019545. Valencia, CA) by following the manufacturer’s protocol. We used Quant-iT RiboGreen quantification kit (Life Technologies, Cat. No. R11490. Carlsbad, CA) quantified the RNA and stored it at -80°C until the library preparation.
We used 200 ng of total RNA and performed RNA-seq library preparation following Lee et al (doi:10.1101/032920 and Gene Expression Omnibus GSE73920). Briefly, PolyA+ selection was done using Dynabeads Oligo(dT)25 (Life technologies, Grand Island, NY), mRNA was fragmented, and RT was performed with the second strand synthesis by incorporating dUTPs. We used External RNA control consortium spike-ins pools 78A and 78B (SRM2374, Zook et al., 2012. PMID: 22859977) transcribed from standard reference. We used barcoded adaptors for indexing the libraries (Qiagen, 98 TruSeq v2 kit barcoded adaptors, Valencia, CA). We sequenced eight multiplexed libraries using a single-ended 50 bp strategy on one lane using a HiSeq Illumina 2500 (Illumina, San Diego, CA).

tag: genotype

tag: condition

value: female

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion.


title: RNAseq.AC7.RNA.WT.DMSO.Rep1

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

description: genotype: wild type_treatment: DMSO

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq and ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut and Tag libraries, the CutRunTools pipeline was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bw: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million.
Supplementary_files_format_and_content: *.ReadsPerGene.txt: Gene count tables give raw read counts mapped to exons of given genes.

organism: Homo sapiens

source_name: cancer cell line

growth_protocol: AC7 cells were grown in DMEM (Gibco, 11960-44), supplemented with 15% FBS, 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122). BT549 cells were grown in RPMI (Gibco, 21870-076), supplemented with 10% FBS, 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122).

extract_protocol:
ChIP-seq protocol: Cells were trypsinized, washed with room temperature PBS twice to remove trypsin, and divided into 40 million-cell aliquots. Cells were fixed using 1% formaldehyde (Sigma Aldrich) for 10 min at 37 °C with constant stirring to keep cells in solution, and finally quenched with 125 mM glycine for 5 min at 37 °C. Quenched cells were washed with cold PBS, and stored in 10-million aliquots at −80 °C until they were used. 10 millions cells were used per epitope in subsequent chromatin immunoprecipitations. Following nuclei extraction, chromatin was sonicated using a Covaris E220 Focused-Ultrasonicator system. Sonicated chromatin was cleared by centrifugation for 10 min at 10,000 r.p.m. (15,000 g). Soluble fractions were incubated with the indicated antibodies (see antibody list) overnight at 4°C, and captured using Protein G Dynabeads (Thermo Fisher). All ChIP-seq samples received 20 ng of spike-in Drosophila chromatin (Active Motif), and 2 µg spike-in antibody (Active Motif) for normalization post sequencing. Antibody-chromatin complexes were captured with Protein G Dynabeads (Thermo Fisher), washed extensively, eluted, and treated with RNase A (Roche) for 30 min at 37 °C and Proteinase K (Life Technologies) for 3 h at 65 °C. ChIP DNA samples were extracted using SPRI beads (Beckman Coulter Agencourt AMP Xpure), washed with 80% Ethanol, and eluted using 0.1X TE. ChIP DNA samples were stored at -20C before library prep were initiated. All ChIP seq libraries were processed with Illumina’s NEBNext Ultra II DNA library Prep Kit (Followed standard protocols). All ChIP seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing.
ChIP-sequencing libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols.
ATAC-seq protocol: ATAC-seq protocol was adapted from following protocol [cit] with slight modifications covered below. 50,000 - 100,000 cells were trypsinized, and washed with cold PBS to remove trypsin. When appropriate, lysing steps were carried out in 10X bulk. Cell pellets were resuspended in 50μl cold ATAC-seq resuspension buffer (RSB) containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2, supplemented with fresh NP40 (final 0.1% v/v), Tween-20 (final 0.1% v/v), Digitonin (final 0.01% v/v). Resuspended cells were incubated in lysis buffer for 3-5 min on ice. Lysis step was quenched with 1 mL of RSB supplemented with Tween-20 (final 0.1% v/v) and pelleted at 500 g for 10 min at 4°C. Cell pellets were resuspended in 50μl transposition reaction mix containing 25 μl 2X TD buffer, 2.5 μl transposase, 16.5 μl 1X PBS, 0.5 μl 1% digitonin (final 0.01% v/v), 0.5 μl 10% Tween-20 (final 0.1% v/v), and 5 μl water nuclease-free water. Transposition reaction was assembled, mixed, and incubated at 37°C for 30 min with constant shaking of 1,000 RPM on a thermomixer. To purify the tagmented DNA, Qiagen MinElute Reaction Cleanup Kit was used. Standard protocol (Buenrostro et al., 2015) [cit] with 10-12 cycles of amplification was used to amplify tagmented library. ATAC-seq libraries were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing.
ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).
RNA-seq protocol: 1,000,000 cells were trypsinized, and washed with cold PBS to remove trypsin. RNA was purified using the Qiagen RNeasy kit, and further processed in the Illumina TruSeq Stranded mRNA library prep kit with appropriate RNA spike-in to mitigate experimental errors. All RNA-seq samples were analyzed by Tapestation to assess quality, and a Qubit Fluorometer to measure concentration. All RNA seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing. For fresh frozen primary samples, 15-25 mg fresh frozen tissue samples were harvested on ice, and washed with cold PBS. Samples were immediately resuspended in cold Qiagen proprietary RLT buffer. The tissue was initially grinded with in a 1.5mL eppendorf tube with a small pestle, and further homogenized using a QiaShredder. Remaining protocol was followed as done with RNA-seq for the cell cultures.
RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols.
Cut&Tag protocol: CUT&Tag was carried out according to Epicypher’s protocol in 8-strip PCR tube with slight modifications. Concanavalin A coated magnetic beads were activated with Bead Activation Buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were kept at room temperature until used. 100,000 cells were trypsinized, washed with cold PBS to remove trypsin. Cells were lysed sing cold Nuclear Extraction Buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor (Roche). Nuclei samples were incubated with activated Concanavalin A beads at room temperature for 10 min. The nuclei-Concanavalin A bead complex was resuspended in Antibody 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), 0.01% Digitonin, and 500 ng of primary antibody. Following overnight incubation at 4°C, primary antibody was removed, and beads were washed once with Digitonin 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. Secondary antibody were added, and incubated with nuclei-Concanavalin A bead complex for 1 hr at room temperature. Nuclei-Concanavalin A bead complex were washed with Digitonin 150 Buffer twice before resuspension in 50uL cold Digitonin300 Buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. 2.0 µL CUTANA pAG-Tn5 (Epicypher) was added to each sample, and in incubated on a nutator for 1 hr at room temperature. Following incubation, beads were washed with cold Digitonin300 Buffer. Targeted chromatin tagmentation and library amplification were carried out exactly according to Epicypher’s protocol.

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al. 2012). BT549 cells were lentivirally infected with either Empty vector, GFP, or full-length SMARCE1 for 24h and then selected with blasticidin for 5-7 days. Cells were harvested 7 days post-infection. For compound treatments, cells were seeded in 6 well-plate or 10cm dishes depending on the experimental setup. Cells were treated at indicated concentrations over 5-7 days with DMSO controls. Media containing fresh compounds was added on day 3. Cells were harvested for genomics experiments using standard protocol.

tag: cell line

value: wild type

tag: treatment

value: DMSO

tag: ngs approach

value: RNA-seq


title: select_library_replicate2_tile4

city: Copenhagen N

first: Sarah

last: Gersing

address: Ole Maaløes vej 5

country: Denmark

institute: University of Copenhagen

description: Amino acid positions 104-137

library_source: genomic

data_processing:
Library strategy: Tile-Seq
Libraries were sequenced on a NextSeq 550 instrument (Illumina) and base called using the instriment's Real Time Analysis software.
Sequencing reads were converted to fastq format and demultiplexed using BaseSpace Sequence Hub.
Reads were alligned and variants called using the TileSeq mutation count pipeline (https://github.com/RyogaLi/tileseq_mutcount) version 0.5.9
Variant calls from the TileSeq mutation count pipeline were then used for calling protein-level amino acid changes and for calculating the enrichment of variants using the TileSeqMave pipeline (https://github.com/jweile/tileseqMave) version 0.6.0.9000
reference sequence: sequence.txt on the series record contains the sequence used for read alignment.

molecule: genomic DNA

organism: synthetic construct

source_name: Yeast cells

growth_protocol: Following transformation, yeast cells were grown in SC-URA galactose until saturation. Cells were either pelleted and stored at -20C before plasmid DNA extraction to serve as the nonselect condition or used for selection. For selection of GCK activity, cells were grown on solid SC-URA 0.2% glucose for three days at 30C. After selection, cells were pelleted and stored at -20C prior to plasmid DNA extraction to serve as the post-selection samples (select).

extract_protocol:
For each condition (select/nonselect, library/wt, replicate1/replicate2), 9 OD units of cells were used for plasmid DNA extraction using the ChargeSwitch Plasmid Yeast Mini kit (Invitrogen) according to the manufacturer's instructions.
The three regional libraries spanning the GCK sequence (aa 2-171, 172-337, 338-466) were constructed by pooled mutagenesis using NNK-degenerate oligos.

tag: host yeast strain

tag: selection

value: yes

tag: molecule subtype

value: plasmid


title: E8.75_rep1 [ATAC-Seq]

city: Cambridge

country: United Kingdom

description: Wildtype E8.75 embryos

organism: Mus musculus


title: RNAseq.AC7.RNA.WT.50nM.CMP12.Rep2

description: genotype: wild type_treatment: 50nM CMP12

value: 50nM CMP12


title: select_library_replicate2_tile2

description: Amino acid positions 38-69


title: select_library_replicate2_tile1

description: Amino acid positions 2-37


title: RNAseq.AC7.RNA.WT.50nM.CMP12.Rep1


title: select_library_replicate1_tile14

description: Amino acid positions 438-465


title: RNAseq.AC7.RNA.WT.2000nM.dBRD9A.Rep2b

description: genotype: wild type_treatment: 2uM dBRD9A

value: 2uM dBRD9A


title: Donor 3 - M2a

city: Rotterdam

first: Carmen

last: Embregts

address: Wytemaweg 80

department: Department of Viroscience

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Illumina adapter sequences and poly-A stretches were trimmed and remaining sequences were aligned to the reference human genome assembly GRCh38 using HISAT2 v2.1.0
Counts of the alignments were determined using htseq-count v.0.11.2
Minimal filtering was applied to remove genes with zero counts in all samples.
Assembly: Sequences were aligned to the reference human genome assembly GRCh38
Supplementary files format and content: Individual .txt files containing count values for all individual genes.

molecule: total RNA

source_name: Monocyte-derived macrophages

growth_protocol: Monocytes were MACS-sorted from PBMCs from healthy blood donors. Monocytes were differentiated into monocyte-derived macrophages in 96-well plates (10^5 cells/well) in maturation medium (RPMI-1640 supplemented with 10% pooled human serum, 1% v/v GlutaMax, 20 ng/mL macrophage colony-stimulating factor (M-CSF, R&D Systems) for 6 days at 37 degrees with 5% CO2. Medium was replaced every other day.

extract_protocol:
RNA was isolated after the 48-hours polarization period, using the standard protocol of the Rneasy Micro kit (Qiagen), including the on-column DNAse digestion step.
Integrity, purity and concentration of the extracted RNA was determined using a BioAnalyzer and total RNA Pico chips (Agilent). cDNA libraries were prepared from the isolated RNA using the Smart-seq2 method

treatment_protocol: Mature macrophages (after 6 daysd of differentiation from monocytes) were polarized into M1, M2a, M2c macrophages or the “RABV-exposed” phenotype, by incubation for 48 hours with IFN-γ (20 ng/mL, R&D Systems) and LPS (100 ng/mL, Sigma Aldrich), IL-4 (20 ng/mL, R&D Systems), IL-10 (20 ng/mL R&D Systems), or with wild-type RABV (MOI of 10), respectively.

tag: cell type

value: Monocyte-derived macrophages

tag: donor


title: E8.5_rep1 [ATAC-Seq]

description: Wildtype E8.5 embryos


title: Liver, Normal Control, MCS2

city: Shanghai

first: Siran

last: Yue

address: CaiLun Road 1200,

country: China

institute: Shanghai University of traditional Chinese medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by fastp v0.20.1 for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm38 whole genome using STAR v2.7.7a with default parameters.Annotation file of Ensembl release 102  transcriptome gff file was provided to STAR as gene model.
raw reads count aligned to each gene were calculated by FeatureCount v2.0.0
Assembly: mm38
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Liver

extract_protocol:
RNA was isolated from 1-2x10^6 cells stored in TRIzol reagent following manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HGPP treatment

tag: tissue

value: Liver

value: WT

tag: strain

value: MCS + CMC-Na


title: Donor 3 - M2c


title: select_library_replicate1_tile12

description: Amino acid positions 371-404


title: E8.5_rep2 [ATAC-Seq]

description: Wildtype E8.5 embryos


title: E8.5_CRISPR_T_WT [ATAC-Seq]

description: Wildtype E8.5 embryos


title: RNAseq.AC7.RNA.WT.2000nM.dBRD9A.Rep1b


title: Donor 3 - M1


title: Donor 3 - M0


title: select_library_replicate1_tile13

description: Amino acid positions 405-437


title: E8.5_CRISPR_T_KO [ATAC-Seq]

description: Brachyury null E8.5 embryos

value: Brachyury KO


title: RNAseq.AC7.RNA.WT.16nM.CMP12.Rep1

description: genotype: wild type_treatment: 16nM CMP12

value: 16nM CMP12


title: Donor 3 - RABV

value: RABV


title: E8.0_rep1 [ATAC-Seq]

description: Wildtype E8.0 embryos

value: Wildtype


title: RNAseq.AC7.RNA.WT.168nM.CMP12.Rep2

description: genotype: wild type_treatment: 168nM CMP12

value: 168nM CMP12


title: E8.0_rep2 [ATAC-Seq]

description: Wildtype E8.0 embryos


title: select_library_replicate1_tile9

description: Amino acid positions 273-304


title: RNAseq.AC7.RNA.WT.168nM.CMP12.Rep1


title: select_library_replicate1_tile11

description: Amino acid positions 338-370


title: select_library_replicate1_tile10

description: Amino acid positions 305-337


title: Donor 2 - M2a


title: Donor 2 - M2c


title: RNAseq.AC7.RNA.WT.16nM.CMP12.Rep2


title: E7.75_rep1 [ATAC-Seq]

description: Wildtype E7.75 embryos


title: Donor 2 - RABV


title: select_library_replicate1_tile7

description: Amino acid positions 207-240


title: select_library_replicate1_tile8

description: Amino acid positions 241-272


title: RNAseq.AC7.RNA.WT.100nM.CMP12.Rep2b

description: genotype: wild type_treatment: 100nM CMP12

value: 100nM CMP12


title: Donor 2 - M0


title: E7.5_rep1 [ATAC-Seq]

description: Wildtype E7.5 embryos


title: Donor 1 - RABV


title: RNAseq.AC7.RNA.WT.100nM.CMP12.Rep1b

value: wild type


title: Donor 1 - M2a


title: E8.75_rep2 [RNA-seq]

description: Wildtype E8.75 embryos

library_source: transcriptomic single cell


title: select_library_replicate1_tile5

description: Amino acid positions 138-171


title: RNAseq.AC7.RNA.SMARCE1_KO.DMSO.Rep2

description: genotype: SMARCE1 null_treatment: DMSO

value: SMARCE1 null

value: DMSO


title: select_library_replicate1_tile6

description: Amino acid positions 172-206

value: yes


title: RNAseq.AC7.RNA.SMARCE1_KO.DMSO.Rep2b

description: genotype: SMARCE1 null_treatment: DMSO

value: RNA-seq


title: select_library_replicate1_tile4

description: Amino acid positions 104-137

value: plasmid


title: Donor 1 - M2c


title: Donor 1 - M1


title: E8.75_rep1 [RNA-seq]

description: Wildtype E8.75 embryos


title: E8.5_rep2 [RNA-seq]

description: Wildtype E8.5 embryos


title: Donor 2 - M1


title: select_library_replicate1_tile3

description: Amino acid positions 70-103


title: select_library_replicate1_tile2

description: Amino acid positions 38-69


title: RNAseq.AC7.RNA.SMARCE1_KO.DMSO.Rep1b

description: genotype: SMARCE1 null_treatment: DMSO


title: Donor 1 - M0


title: E7.5_rep2 [ATAC-Seq]

description: Wildtype E7.5 embryos


title: E8.5_rep1 [RNA-seq]

description: Wildtype E8.5 embryos


title: E8.5_CRISPR_T_WT [RNA-seq]

description: Wildtype E8.5 embryos


title: RNAseq.AC7.RNA.SMARCE1_KO.50nM.CMP12.Rep2

description: genotype: SMARCE1 null_treatment: 50nM CMP12

value: 50nM CMP12


title: select_library_replicate1_tile1

description: Amino acid positions 2-37


title: RNAseq.AC7.RNA.SMARCE1_KO.50nM.CMP12.Rep1


title: nonselect_library_replicate2_tile14

description: Amino acid positions 438-465

value: no


title: E8.5_CRISPR_T_KO [RNA-seq]

description: Brachyury null E8.5 embryos


title: RNAseq.AC7.RNA.SMARCE1_KO.2000nM.dBRD9A.Rep1b

description: genotype: SMARCE1 null_treatment: 2uM dBRD9A

value: 2uM dBRD9A


title: RNAseq.AC7.RNA.SMARCE1_KO.2000nM.dBRD9A.Rep2b


title: nonselect_library_replicate2_tile13

description: Amino acid positions 405-437


title: E8.0_rep2 [RNA-seq]

description: Wildtype E8.0 embryos


title: nonselect_library_replicate2_tile12

description: Amino acid positions 371-404


title: E7.75_rep1 [RNA-seq]

description: Wildtype E7.75 embryos


title: RNAseq.AC7.RNA.SMARCE1_KO.DMSO.Rep1

description: genotype: SMARCE1 null_treatment: DMSO


title: nonselect_library_replicate2_tile11

description: Amino acid positions 338-370


title: E7.5_rep2 [RNA-seq]

description: Wildtype E7.5 embryos


title: nonselect_library_replicate2_tile10

description: Amino acid positions 305-337


title: nonselect_library_replicate2_tile9

description: Amino acid positions 273-304


title: RNAseq.AC7.RNA.SMARCE1_KO.168nM.CMP12.Rep2

description: genotype: SMARCE1 null_treatment: 168nM CMP12


title: Sample.143.Maui's dolphin.203867110002_R06C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Skin species=Cephalorhynchus hectori maui

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Cephalorhynchus hectori maui

source_name: Skin

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: basename

tag: species common name

value: Maui's dolphin

tag: female

tag: canbeusedforagingstudies


title: RNAseq.AC7.RNA.SMARCE1_KO.16nM.CMP12.Rep1

description: genotype: SMARCE1 null_treatment: 16nM CMP12


title: Sample.142.Maui's dolphin.203867110002_R05C02


title: E7.5_rep1 [RNA-seq]

description: Wildtype E7.5 embryos

tag: background


title: Sample.140.Beluga whale.203867110002_R03C02

description: genomic DNA methylation from tissue=Skin species=Delphinapterus leucas

organism: Delphinapterus leucas

value: Beluga whale


title: E8.0_rep1 [RNA-seq]

description: Wildtype E8.0 embryos

tag: genotype


title: RNA-seq of heart_KO_rep2

city: shenzhen

first: Liang

last: Fang

address: Shenzhen, Guangdong

department: Department of Biology

institute: Southern University of Science and Technology

data_processing:
The RNA-seq reads were trimmed for adaptor sequence using cutadapt, then mapped to mm10 reference genome by HISAT2 version 2.1.0 with the default parameters.
Read counts were generated using featureCounts version 2.0.1 with parameters -T 8 -s 2 -p -B -C -t exon -g gene_id --extraAttributes gene_name.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse tissue

extract_protocol:
Total RNA was isolated using RNA Isolator Total RNA Extraction Reagent (Vazyme) followed by isopropanol precipitation according to standard protocols.
Libraries were prepared using standard protocol provided by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme).

value: NSUN6 KO

value: heart


title: RNAseq.AC7.RNA.SMARCE1_KO.168nM.CMP12.Rep1


title: RNA-seq of heart_KO_rep1


title: RNAseq.AC7.RNA.SMARCE1_KO.100nM.CMP12.Rep2b

description: genotype: SMARCE1 null_treatment: 100nM CMP12


title: RNAseq.AC7.RNA.SMARCE1_KO.16nM.CMP12.Rep2

value: 16nM CMP12


title: nonselect_library_replicate2_tile7

description: Amino acid positions 207-240


title: Sample.141.Beluga whale.203867110002_R04C02


title: RNA-seq of heart_WT_rep2

value: WT


title: nonselect_library_replicate2_tile8

description: Amino acid positions 241-272


title: nonselect_library_replicate2_tile6

description: Amino acid positions 172-206


title: Sample.138.Beluga whale.203867110002_R01C02


title: RNA-seq of heart_WT_rep1


title: RNAseq.AC7.RNA.SMARCE1_KO.100nM.CMP12.Rep1b


title: RNAseq.AC7.RNA.Parental.Rep2

description: genotype: wild type


title: nonselect_library_replicate2_tile5

description: Amino acid positions 138-171


title: Sample.136.Beluga whale.203867110002_R05C01


title: nonselect_library_replicate2_tile4

description: Amino acid positions 104-137


title: RNAseq.AC7.RNA.NF2.Null.Rep2

description: genotype: NF2 null

value: NF2 null


title: Sample.135.Beluga whale.203867110002_R04C01


title: RNA-seq of kidney_KO_rep1

value: kidney


title: Sample.134.Beluga whale.203867110002_R03C01


title: nonselect_library_replicate2_tile3

description: Amino acid positions 70-103


title: RNA-seq of kidney_WT_rep1


title: Sample.139.Beluga whale.203867110002_R02C02


title: RNAseq.AC7.RNA.NF2.Null.Rep1

description: genotype: NF2 null


title: Sample.137.Beluga whale.203867110002_R06C01


title: RNA-seq of kidney_WT_rep2


title: Sample.133.Beluga whale.203867110002_R02C01


title: nonselect_library_replicate2_tile1

description: Amino acid positions 2-37


title: nonselect_library_replicate1_tile14

description: Amino acid positions 438-465


title: RNA-seq of spleen_KO_rep2

value: spleen


title: RNAseq.AC7.RNA.Parental.Rep1

description: genotype: wild type

value: wild type


title: RNAseq.AC7.RNA.Clone29.SMARCE1.Null.Rep2

description: genotype: SMARCE1 null

value: SMARCE1 null


title: RNAseq.AC7.RNA.Clone38.WT.Control.Rep1

description: genotype: wild type


title: RNAseq.AC7.RNA.Clone29.SMARCE1.Null.Rep1

description: genotype: SMARCE1 null


title: nonselect_library_replicate1_tile13

description: Amino acid positions 405-437


title: Sample.132.Beluga whale.203867110002_R01C01

value: yes


title: RNA-seq of spleen_KO_rep1


title: RNAseq.AC7.RNA.Clone21.SMARCE1.Null.Rep2

description: genotype: SMARCE1 null

value: RNA-seq


title: nonselect_library_replicate1_tile12

description: Amino acid positions 371-404

value: plasmid


title: Sample.131.Beluga whale.203867110004_R06C02


title: Sample.127.Beluga whale.203867110004_R02C02


title: Sample.129.Beluga whale.203867110004_R04C02


title: Sample.130.Beluga whale.203867110004_R05C02


title: Sample.128.Beluga whale.203867110004_R03C02


title: RNAseq.AC7.RNA.Clone21.SMARCE1.Null.Rep1

description: genotype: SMARCE1 null


title: nonselect_library_replicate1_tile11

description: Amino acid positions 338-370


title: nonselect_library_replicate1_tile10

description: Amino acid positions 305-337


title: RNA-seq of liver_KO_rep2

value: liver


title: RNA-seq of spleen_WT_rep2


title: RNAseq.AC7.RNA.Clone17.WT.Control.Rep2

description: genotype: wild type


title: RNAseq.AC7.RNA.Clone17.WT.Control.Rep1

description: genotype: wild type


title: RNA-seq of liver_KO_rep1


title: RNA-seq of liver_WT_rep2


title: Sample.126.Beluga whale.203867110004_R01C02


title: RNA-seq of spleen_WT_rep1


title: Sample.125.Beluga whale.203867110004_R06C01


title: Sample.123.Beluga whale.203867110004_R04C01


title: RNA-seq of small_intestine_KO_rep2

description: small intestine_KO2

value: small intestine


title: RNA-seq of liver_WT_rep1


title: CutAndTag.AC7.SS18.WT

description: genotype: wild type

data_processing:
Library strategy: CUT&Tag
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation, and ChIPseq reads were aligned with Bowtie2 v2.29 in the -k 1 reporting mode.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ChIPseq and ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut and Tag libraries, the CutRunTools pipeline was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.bw: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million.
Supplementary_files_format_and_content: *.ReadsPerGene.txt: Gene count tables give raw read counts mapped to exons of given genes.

tag: antibody

value: Rabbit anti-SS18 (D6I4Z); 21792S

value: CutAndTag


title: nonselect_library_replicate1_tile6

description: Amino acid positions 172-206

value: no


title: nonselect_library_replicate1_tile8

description: Amino acid positions 241-272


title: nonselect_library_replicate1_tile9

description: Amino acid positions 273-304


title: RNA-seq of small_intestine_KO_rep1

description: small intestine_KO1

value: NSUN6 KO


title: Sample.124.Beluga whale.203867110004_R05C01

value: Beluga whale


title: nonselect_library_replicate1_tile5

description: Amino acid positions 138-171


title: RNAseq.AC7.RNA.Clone15.WT.Control.Rep1

description: genotype: wild type

tag: cell line


title: Sample.122.Beluga whale.203867110004_R03C01


title: RNA-seq of small_intestine_WT_rep2

description: small intestine_WT2

tag: treatment


title: Sample.121.Beluga whale.203867110004_R02C01


title: CutAndTag.AC7.SS18.SMARCE1_KO

description: genotype: SMARCE1 null

tag: ngs approach


title: RNAseq.AC7.RNA.Clone15.WT.Control.Rep2

description: genotype: wild type


title: CutAndTag.AC7.SMARCD1.WT

description: genotype: wild type

value: Mouse anti-BAF60A(23); SC135843


title: nonselect_library_replicate1_tile4

description: Amino acid positions 104-137

tag: host yeast strain


title: nonselect_library_replicate1_tile3

description: Amino acid positions 70-103

tag: selection


title: RNA-seq of small_intestine_WT_rep1

description: small intestine_WT1

value: WT


title: nonselect_library_replicate1_tile7

description: Amino acid positions 207-240

tag: molecule subtype


title: CutAndTag.AC7.SMARCD1.SMARCE1_KO

description: genotype: SMARCE1 null


title: Sample.118.Beluga whale.203867110001_R05C02


title: Sample.120.Beluga whale.203867110004_R01C01


title: CutAndTag.AC7.SMARCC1.WT

description: genotype: wild type

value: Rabbit anti-SMARCC1/BAF155 (D7F8S); 11956S


title: mRNA-BisSeq of heart_KO_rep2

data_processing:
RNA-m5C pipeline
Assembly: mm10
Supplementary files format and content: txt, m5C sites
Library strategy: mRNA bisulfite sequencing

source_name: tissue

extract_protocol:
Total RNA was extracted by TRIzol® Reagent (Ambion). mRNA was enriched using VAHTS mRNA Capture Beads (Vazyme, #N401). 200 ng mRNA was converted by EZ RNA methylation kit (Zymo Research) according to the manufacturer’s protocol with minor modification. More specifically, mRNA was incubated at 70 °C for 10 min, and 60 °C for 1 h. Converted RNA was then reverse transcribed into cDNA using HiScript II Q Select RT SuperMix (Vazyme, #R233-01).
VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme)

value: heart


title: nonselect_library_replicate1_tile2

description: Amino acid positions 38-69


title: nonselect_library_replicate1_tile1

description: Amino acid positions 2-37


title: mRNA-BisSeq of heart_WT_rep2


title: Sample.117.Beluga whale.203867110001_R04C02


title: CutAndTag.AC7.SMARCC1.SMARCE1_KO

description: genotype: SMARCE1 null


title: Sample.115.Beluga whale.203867110001_R02C02


title: Sample.119.Beluga whale.203867110001_R06C02


title: Sample.116.Beluga whale.203867110001_R03C02


title: CutAndTag.AC7.IgG.WT

description: genotype: wild type

value: IgG


title: CutAndTag.AC7.SMARCB1.SMARCE1_KO

description: genotype: SMARCE1 null


title: CutAndTag.AC7.SMARCB1.WT

description: genotype: wild type

value: wild type


title: mRNA-BisSeq of kidney_KO_rep1

value: kidney


title: mRNA-BisSeq of kidney_KO_rep2


title: mRNA-BisSeq of heart_KO_rep1


title: CutAndTag.AC7.SMARCE1.WT

description: genotype: wild type

value: Rabbit anti-BAF57/SMARCE1 ; ab70540


title: mRNA-BisSeq of kidney_WT_rep2


title: CutAndTag.AC7.SMARCE1.SMARCE1_KO

description: genotype: SMARCE1 null

value: SMARCE1 null


title: mRNA-BisSeq of spleen_KO_rep2

value: spleen


title: mRNA-BisSeq of heart_WT_rep1


title: mRNA-BisSeq of kidney_WT_rep1


title: CutAndTag.AC7.DPF2.WT

description: genotype: wild type

value: Rabbit anti-DPF2/REQ [EPR9206(B)]; ab134942


title: Sample.114.Beluga whale.203867110001_R01C02

value: yes


title: mRNA-BisSeq of spleen_KO_rep1


title: CutAndTag.AC7.BRG1.WT

description: genotype: wild type

value: Rabbit anti-SMARCA4 (EPNCIR111A); ab110641


title: Sample.113.Beluga whale.203867110001_R06C01


title: mRNA-BisSeq of spleen_WT_rep2


title: Sample.111.Beluga whale.203867110001_R04C01


title: Sample.110.Beluga whale.203867110001_R03C01


title: CutAndTag.AC7.BRG1.SMARCE1_KO

description: genotype: SMARCE1 null

value: CutAndTag


title: Sample.112.Beluga whale.203867110001_R05C01


title: CutAndTag.AC7.ACTL6A.WT

description: genotype: wild type

value: Rabbit anti-BAF53A; A301-391A


title: mRNA-BisSeq of spleen_WT_rep1


title: mRNA-BisSeq of liver_KO_rep2

value: NSUN6 KO

value: liver


title: Sample.108.Beluga whale.203867110001_R01C01

value: Beluga whale


title: CutAndTag.AC7.ACTL6A.SMARCE1_KO

description: genotype: SMARCE1 null


title: Sample.109.Beluga whale.203867110001_R02C01


title: mRNA-BisSeq of liver_KO_rep1


title: CutAndTag.AC7.DPF2.SMARCE1_KO

description: genotype: SMARCE1 null


title: CutAndTag.AC7.250A.WT

description: genotype: wild type

value: Rabbit anti-ARID1A/BAF250A (D2A8U); 11956S


title: mRNA-BisSeq of liver_WT_rep2

value: WT


title: CutAndTag.AC7.250A.SMARCE1_KO

description: genotype: SMARCE1 null


title: ChIPseq.BT549.SS18.SMARCE1.WT

description: lentivirus: full length SMARCE1

tag: lentivirus

value: full-length SMARCE1

value: Rabbit anti-SS18 (D6I4Z); 21792S

value: ChIP-seq


title: Sample.106.Beluga whale.203867110003_R05C02


title: Sample.105.Beluga whale.203867110003_R04C02


title: Sample.107.Beluga whale.203867110003_R06C02


title: mRNA-BisSeq of small_intestine_KO_rep2

value: small intestine


title: Sample.103.Beluga whale.203867110003_R02C02


title: ChIPseq.BT549.SMARCE1.SMARCE1.WT

description: lentivirus: full length SMARCE1

value: Rabbit anti-BAF57/SMARCE1 ; ab70540


title: mRNA-BisSeq of small_intestine_KO_rep1


title: mRNA-BisSeq of small_intestine_WT_rep2


title: ChIPseq.BT549.SMARCE1.GFP

description: lentivirus: full length GFP

value: full-length GFP


title: Sample.104.Beluga whale.203867110003_R03C02


title: mRNA-BisSeq of small_intestine_WT_rep1


title: Sample.102.Beluga whale.203867110003_R01C02


title: ChIPseq.BT549.SMARCC1.Naïve

description: lentivirus: Empty

value: Empty

value: Rabbit anti-SMARCC1/BAF155 (D7F8S); 11956S


title: WT.SpibKO.Sox8KO.AireKO.Pdpn-CD104-.mTEClo.rep1-4_HASH

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: 11 samples (4 WT, 2 SpibKO, 2 Sox8KO and 3 AireKO) were hashed together into a single 10X scRNA-seq run

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as transcript-by-cell matrices using Cell Ranger (v6.1.0, 10X Genomics).
Hash-by-cell matrices were computed using CITE-seq-count (v1.4.3).
Cells with no or multiple hashes, high mitochondrial content, or lineage markers of contaminants (i.e., T, endothelial cells) were filtered out in Seurat (v4.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: tsv files for barcodes, features and counts for gene expression and hash matrices, and txt files indicating retained cells with their hash assignment

source_name: Thymus

extract_protocol:
mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, hashing with TotalSeq antibodies against H2-Kb and CD29 (adult/perinate expt) or just H2-Kb (WT/Spib/Sox8/Aire expt), and flow sorting mTECs into DMEM/10%FCS.
Purified cells were sent to the Broad Institute Genomics Platform, which performed encapsulation and RNA and hash library preparation following 10X Genomics protocols (3' v3 chemistry)

tag: cell type

value: mTEClo


title: mRNA-BisSeq of liver_WT_rep1

tag: tissue


title: RNAseq.AC7.RNA.Clone38.WT.Control.Rep2

description: genotype: wild type

value: wild type

value: RNA-seq


title: ChIPseq.BT549.SMARCA4.Naïve

description: lentivirus: Empty

value: Rabbit anti-SMARCA4 (EPNCIR111A); ab110641


title: AireKO.mTEChi.rep#2

data_processing:
Sequenced libraries were demultiplexed, assigned to individual cells, and aligned to the mm10 genome using Cell Ranger ATAC (v1.1.0, 10X Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: tsv of mapped fragments

extract_protocol:
Cells were processed following the 10X Genomics scATAC-seq protocol. Briefly, ~50,000 sorted mTECs were spun down and examined for cell number and viability. Nuclei were isolated in 50ul ice-cold lysis buffer (10mM Tris-HCl [pH 7.4], 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% digitonin, 1% bovine serum albumin) for 5 minutes (first replicate) or 1 minute (second replicate). Nuclei were washed and resuspended in nuclei buffer to target 5,000 recovered nuclei per replicate.
Nuclei were transposed at 37°C for 60 minutes, loaded into gel beads-in-emulsion, and incubated for linear amplification. Barcoded single nucleus fragments were purified and amplified by polymerase chain reaction (PCR; 12 cycles).

treatment_protocol: mTEChi were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies and flow sorting mTECs into DMEM/10%FCS.

tag: strain

value: AireKO

value: mTEChi


title: ChIPseq.BT549.SMARCC1.DOX.N102.V5.SMARCE1

description: lentivirus: full length SMARCE1


title: ChIPseq.BT549.SS18.GFP

description: lentivirus: full length GFP


title: WT.SpibKO.Sox8KO.AireKO.Pdpn-CD104-.mTEClo.rep1-4_GEX


title: AireKO.mTEChi.rep#1


title: Sample.98.Beluga whale.203867110003_R03C01

tag: basename

value: Beluga whale

value: yes


title: ChIPseq.BT549.SMARCA4.DOX.N102.V5.SMARCE1

description: lentivirus: full length SMARCE1


title: nonselect_library_replicate2_tile2

description: Amino acid positions 38-69

value: no

value: plasmid


title: Sample.100.Beluga whale.203867110003_R05C01

tag: species common name


title: Sample.101.Beluga whale.203867110003_R06C01

tag: female


title: ChIPseq.BT549.Input.Naïve

description: lentivirus: Empty


title: AireWT.mTEChi.rep#2

value: AireWT


title: RNA-seq of kidney_KO_rep2

value: NSUN6 KO

value: kidney


title: ChIPseq.BT549.Input.DOX.N102.V5.SMARCE1

description: lentivirus: full length SMARCE1

value: full-length SMARCE1

value: ChIP-seq


title: AireWT.mTEChi.rep#1


title: Grhl1.mTEC.rep#3

description: CUT&Tag

data_processing:
Library strategy: CUT&Tag
Low quality reads were discared using Trimmomatic (v0.36)
Reads were mapped to the mouse reference genome (mm10) with bowtie2 (v2.29) using parameters --local --very-sensitive -no-mixed --no-discordant -I 10 -X 700
Bam files were generated and multimapping reads removed by samtools (v1.3.1), and duplicate reads were removed by picard (v2.8.0)
Bigwig files were generated using deeptools (v3.0.2) with counts-per-million normalization
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
mTECs were washed in wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), bound to concavalin A beads (Bangs Laboratories), permeabilized in wash buffer plus 0.05% digitonin, and incubated overnight with 1:50 primary antibody (anti-H3K27ac [Abcam], -Hnf4α [Abcam], -Grhl1 [Novus], -Pou2f3 [Sigma], or -IgG [Rockland]) at 4°C in wash buffer plus 0.05% digitonin, 2mM EDTA and 0.1% BSA. The next day, H3K27ac, Grhl1, IgG, and some Pou2f3 samples were lightly fixed with 0.1% paraformaldehyde at room temperature for 2 minutes before proceeding. (We and others have observed improved CUT&Tag signal-to-noise ratio for some TFs with light fixation.) Samples were incubated with secondary antibody (guinea pig anti-rabbit [Rockland] for H3K27ac, Grhl1, Pou2f3, and IgG; rabbit anti-mouse [Abcam] for Hnf4α) at 1:100 for 1 hour at room temperature in wash buffer plus 0.05% digitonin. Samples were washed and incubated with pA-Tn5 (Addgene #124601, gift from Steve Henikoff, purified in-house) at 1:200 for 1 hour at room temperature in 300mM NaCl wash buffer plus 0.01% digitonin. Samples were washed twice then tagmented for 1 hour at 37°C in 300mM NaCl wash buffer plus 0.01% digitonin and 10mM MgCl.
Tagmentation was halted with EDTA, sodium dodecyl sulfate and proteinase K for 1 hour at 55°C. Tagmented DNA was phenol-chloroform extracted and amplified by PCR with NEBNext 2X Master Mix (NEB) using the following program: 72°C for 2min, 98°C for 30s, 16 cycles of 98°C for 10s and 63°C for 10s, 72°C for 1min, hold. Amplified libraries were quantified by Qubit (Thermo) and Tapestation (Agilent).

treatment_protocol: mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, and flow sorting mTECs into DMEM/10%FCS.

value: WT

value: mTEC


title: Grhl1.mTEC.rep#2

description: CUT&Tag


title: ChIPseq.BT549.H3K4me3.GFP

description: lentivirus: full length GFP

value: full-length GFP

value: Rabbit anti-Histone H3 (tri methyl K4) ; ab8580


title: ChIPseq.BT549.H3K4me3.SMARCE1.WT

description: lentivirus: full length SMARCE1


title: Sample.96.Beluga whale.203867110003_R01C01

tag: canbeusedforagingstudies


title: Sample.94.Beluga whale.202897220122_R05C02


title: Grhl1.mTEC.rep#1

description: CUT&Tag


title: ChIPseq.BT549.H3K27ac.GFP

description: lentivirus: full length GFP

value: Rabbit anti-Histone H3 (acetyl K27); ab4729


title: Sample.93.Beluga whale.202897220122_R04C02


title: ChIPseq.BT549.ARID2.SMARCE1.WT

description: lentivirus: full length SMARCE1

value: Rabbit anti-ARID2 (D8D8U); 82342S


title: Hnf4a.mTEC.rep#4

description: CUT&Tag


title: ChIPseq.BT549.ARID2.GFP

description: lentivirus: full length GFP


title: Hnf4a.mTEC.rep#2

description: CUT&Tag


title: Sample.95.Beluga whale.202897220122_R06C02


title: ChIPseq.BT549.ARID1A.SMARCE1.WT

description: lentivirus: full length SMARCE1

value: Rabbit anti-ARID1A/BAF250A (D2A8U); 11956S


title: Hnf4a.mTEC.rep#3

description: CUT&Tag


title: Sample.99.Beluga whale.203867110003_R04C01


title: ChIPseq.BT549.H3K27ac.SMARCE1.WT

description: lentivirus: full length SMARCE1

value: Rabbit anti-Histone H3 (acetyl K27); ab4730


title: Sample.97.Beluga whale.203867110003_R02C01

value: Beluga whale


title: ChIPseq.BT549.ARID1A.GFP

description: lentivirus: full length GFP


title: Hnf4a.mTEC.rep#1

description: CUT&Tag


title: Sample.88.Maui's dolphin.202897220122_R05C01

value: Maui's dolphin

value: yes


title: Sample.89.Maui's dolphin.202897220122_R06C01


title: Sample.90.Maui's dolphin.202897220122_R01C02


title: scRNA-Seq_P3 lung peripheral cells

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

description: Control lungs

data_processing:
10X Cell Ranger software version 5.0 was used to align reads to the mouse genome;
R package Seurat (version 3.2.2) was used for single cell transcriptome analysis;
SCTransform normalization method was used to control for  between-sample sequencing depth variation;
Cells were removed according to the following  thresholds: <300 genes/cell or >5000 genes per cell, >20000 UMIs/cell, 15% mitochondrial  content, <0.01% hemoglobin content;
For DEG analysis between comparison groups, genes were detected  if expressed in at least 5% of cells in the group with a log fold change of at least 0.25.

source_name: Postnatal lung

extract_protocol: Cells were sorted from P3 lung peripheral. The FACS-sorted single cells were loaded onto 3′ library chips according to the manufacturer's protocol for Chromium 10X Single Cell 3′ Library v3.

value: Wild type

value: Sorted peripheral lung single cells

tag: Stage

value: Postnatal day 3


title: Sample.91.Humpback whale.202897220122_R02C02

description: genomic DNA methylation from tissue=Skin species=Megaptera novaeangliae

organism: Megaptera novaeangliae

value: Humpback whale


title: Sample.92.Beluga whale.202897220122_R03C02


title: Gr8_D14_TM2_CD8

type: RNA

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

description: RNA of splenic CD3+ CD8+ T cells

hyb_protocol: 2µg of total RNA were used for the One-Cycle target labeling assay, further processed and hybridized to the GeneChip® Mouse 430 2.0 array from Affymetrix according to manufacturer’s instructions.

scan_protocol: The Arrays were washed using Affymetrix fluidics station FS450, and scanned using the Gene Chip Scanner 3000.

data_processing: BRB Array Tools

label: biotin

source_name: Mouse CD3+ CD8+ T cells  from spleen 14 days after TxT with MDSC treatment

label_protocol: One Cycle Target Labelling Protocol

extract_protocol: RNA was isolated using the Direct-zol™ RNA Mini Prep Kit (Zymo Research, Freiburg)

treatment_protocol: Please see Kustermann et al. 2019 -  https://doi.org/10.1038/s41598-019-44419-5, Hüsecken et al. 2017 - https://doi.org/10.1038/s41598-017-13019-6 for detailed methods: 1) Isolation of cells. Spleen +  2) RNA preparation

value: mouse spleen


title: Gr8_D14_TM1_CD8

description: RNA of splenic CD3+ CD8+ T cells

source_name: Mouse CD3+ CD8+ T cells from spleen  14 days after TxT with MDSC treatment


title: Sample.85.Maui's dolphin.202897220122_R02C01


title: Sample.84.Maui's dolphin.202897220122_R01C01


title: B2-mm_E-6

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

data_processing:
Alignment (HISAT2 2.1.0), Counting (featureCounts - 2.0.0)
Annotation with Ensembl 101
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing raw counts obtained after counting with featureCounts

source_name: Mouse aortic vascular smooth muscle cells

growth_protocol: Cells were cultivated in DMEM media, supplemented with 10% FCS, 0.14 IU insulin, 10 µg/L EGF, 5 mg/L transferrin, 100 nM hydrocortison and 30 nM sodium selenite.

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
polyA enrichment (performed by Novogene Europe)

treatment_protocol: Cells were synchronized for 24h in DMEM media without any supplementation ("- media") and then incubated for 24h or 48h with 10µg/L EGF, 10nM Angiotensin II and/or 1µM U46619, diluted in "-" media.

value: aVSMC

tag: mouse id used for cell isolation

tag: treatment type

value: 10ug/L EGF

tag: treatment length


title: Gr7_D14_T2_CD8

description: RNA of splenic CD3+ CD8+ T cells

source_name: Mouse CD3+ CD8+ T cells from spleen 14 days after TxT without MDSC treatment


title: B2-mm_C-6

value: Control


title: Gr8_D14_TM3_CD8

description: RNA of splenic CD3+ CD8+ T cells

source_name: Mouse CD3+ CD8+ T cells from spleen 14 days after TxT with MDSC treatment


title: Gr7_D14_T3_CD8

description: RNA of splenic CD3+ CD8+ T cells

source_name: Mouse CD3+ CD8+ T cells from spleen  14 days after TxT without MDSC treatment


title: Sample.87.Maui's dolphin.202897220122_R04C01


title: Sample.83.Maui's dolphin.202897220123_R06C02


title: Sample.86.Maui's dolphin.202897220122_R03C01


title: ChIPseq.AC7.SMARCA4.WT

description: genotype: wild type

tag: cell line

tag: genotype

value: wild type

tag: antibody

value: Rabbit anti-SMARCA4 (EPNCIR111A); ab110641

value: ChIP-seq


title: ChIPseq.AC7.SS18.SMARCE1_KO

description: genotype: SMARCE1 null

value: SMARCE1 null

value: Rabbit anti-SS18 (D6I4Z); 21792S

tag: ngs approach


title: ChIPseq.AC7.SS18.WT

description: genotype: wild type


title: B2-mm_A-6

value: 10nM AngII


title: Gr6_D14_TM3_CD4

description: RNA of splenic CD3+ CD4+ T cells

source_name: Mouse CD3+ CD4+ T cells from spleen 14 days after TxT with MDSC treatment


title: ChIPseq.AC7.SMARCA4.SMARCE1_KO

description: genotype: SMARCE1 null


title: B2-mm_EA-5

value: 10ug/L EGF + 10nM AngII


title: ChIPseq.AC7.POL2.WT

description: genotype: wild type

value: Mouse anti-Pol II ; C15100055


title: ChIPseq.AC7.POL2.SMARCE1_KO

description: genotype: SMARCE1 null


title: Sample.81.Maui's dolphin.202897220123_R04C02

value: Maui's dolphin

value: yes


title: ChIPseq.AC7.Input.WT

description: genotype: wild type


title: Sample.82.Maui's dolphin.202897220123_R05C02


title: B2-mm_E-5


title: B2-mm_C-5


title: B2-mm_A-5


title: Gr6_D14_TM2_CD4

description: RNA of splenic CD3+ CD4+ T cells


title: ChIPseq.AC7.Input.SMARCE1_KO

description: genotype: SMARCE1 null


title: Sample.79.Blue whale.202897220123_R02C02

description: genomic DNA methylation from tissue=Skin species=Balaenoptera musculus

organism: Balaenoptera musculus

value: Blue whale


title: B2-mm_EA-4


title: ChIPseq.AC7.SMARCE1.WT

description: genotype: wild type

value: Rabbit anti-BAF57/SMARCE1 ; ab70540


title: Gr6_D14_TM1_CD4

description: RNA of splenic CD3+ CD4+ T cells


title: Gr5_D14_T3_CD4

description: RNA of splenic CD3+ CD4+ T cells

source_name: Mouse CD3+ CD4+ T cells from spleen  14 days after TxT without MDSC treatment


title: Sample.80.Sperm whale.202897220123_R03C02

description: genomic DNA methylation from tissue=Skin species=Physeter macrocephalus

organism: Physeter macrocephalus

value: Sperm whale


title: Sample.78.Beluga whale.202897220123_R01C02

value: Beluga whale


title: Sample.75.Beluga whale.202897220123_R03C01


title: Sample.77.Beluga whale.202897220123_R05C01


title: Sample.76.Beluga whale.202897220123_R04C01


title: Gr5_D14_T2_CD4

description: RNA of splenic CD3+ CD4+ T cells

source_name: Mouse CD3+ CD4+ T cells from spleen 14 days after TxT without MDSC treatment

value: mouse spleen


title: Gr4_D7_TM1_CD8

description: RNA of splenic CD3+ CD8+ T cells

source_name: Mouse CD3+ CD8+ T cells from spleen 7 days after TxT with MDSC treatment


title: ChIPseq.AC7.SMARCE1.SMARCE1_KO

description: genotype: SMARCE1 null

source_name: cancer cell line


title: B2-mm_E-4

value: aVSMC

value: 10ug/L EGF


title: ChIPseq.AC7.H3K4me3.WT

description: genotype: wild type

value: wild type

value: Rabbit anti-Histone H3 (tri methyl K4) ; ab8580


title: B2-mm_C-4

value: Control


title: Gr5_D14_T1_CD4

description: RNA of splenic CD3+ CD4+ T cells


title: B2-mm_E-2


title: B2-mm_EA-2


title: ChIPseq.AC7.H3K27Ac.WT

description: genotype: wild type

value: Rabbit anti-Histone H3 (acetyl K27); ab4730

value: ChIP-seq


title: Gr4_D7_TM2_CD8

description: RNA of splenic CD3+ CD8+ T cells


title: Gr3_D7_T1_CD8

description: RNA of splenic CD3+ CD8+ T cells

source_name: Mouse CD3+ CD8+ T cells from spleen 7 days after TxT without MDSC treatment


title: Gr3_D7_T3_CD8

description: RNA of splenic CD3+ CD8+ T cells


title: Sample.72.Beluga whale.202897220087_R06C02

source_name: Skin


title: Sample.73.Beluga whale.202897220123_R01C01


title: ChIPseq.AC7.DPF2.WT

description: genotype: wild type

value: Rabbit anti-DPF2/REQ [EPR9206(B)]; ab134942


title: Gr2_D7_TM3_CD4

description: RNA of splenic CD3+ CD4+ T cells

source_name: Mouse CD3+ CD4+ T cells from spleen 7 days after TxT with MDSC treatment


title: Sample.71.Beluga whale.202897220087_R05C02


title: ChIPseq.AC7.H3K27Ac.SMARCE1_KO

description: genotype: SMARCE1 null

value: SMARCE1 null

value: Rabbit anti-Histone H3 (acetyl K27); ab4729


title: ChIPseq.AC7.H3K4me3.SMARCE1_KO

description: genotype: SMARCE1 null


title: B2-mm_A-4

value: 10nM AngII


title: Sample.70.Beluga whale.202897220087_R04C02

value: yes


title: B2-mm_C-2


title: Sample.74.Beluga whale.202897220123_R02C01


title: Gr3_D7_T2_CD8

description: RNA of splenic CD3+ CD8+ T cells


title: ChIPseq.AC7.DPF2.SMARCE1_KO

description: genotype: SMARCE1 null


title: Sample.69.Beluga whale.202897220087_R03C02


title: B2-mm_A-2


title: Gr2_D7_TM1_CD4

description: RNA of splenic CD3+ CD4+ T cells


title: Gr2_D7_TM2_CD4

description: RNA of splenic CD3+ CD4+ T cells


title: Sample.68.Beluga whale.202897220087_R02C02


title: B2-mm_EA-1

value: 10ug/L EGF + 10nM AngII


title: Sample.67.Beluga whale.202897220087_R01C02


title: Gr1_D7_T2_CD4

description: RNA of splenic CD3+ CD4+ T cells

source_name: Mouse CD3+ CD4+ T cells from spleen 7 days after TxT without MDSC treatment


title: Gr1_D7_T3_CD4

description: RNA of splenic CD3+ CD4+ T cells


title: ChIPseq.AC7.CTCF.WT

description: genotype: wild type

value: Rabbit anti-CTCF (D31H2); 3418S


title: ChIPseq.AC7.CTCF.SMARCE1_KO

description: genotype: SMARCE1 null


title: B2-mm_EA-6


title: B2-mm_E-1


title: B1-mm_U-5


title: B2-mm_C-1


title: B2-mm_A-1


title: B1-mm_EU-5


title: ChIPseq.AC7.BRD9.SMARCE1_KO

description: genotype: SMARCE1 null

value: Rabbit anti-BRD9; 61537


title: ChIPseq.AC7.ARID1A.SMARCE1_KO

description: genotype: SMARCE1 null

value: Rabbit anti-ARID1A/BAF250A (D2A8U); 11956S


title: Sample.65.Beluga whale.202897220087_R05C01

value: Beluga whale


title: ATACseq.BT549.ATAC.SMARCE1.WT.Rep2

description: lentivirus: full length SMARCE1

value: full-length SMARCE1

value: ATAC-seq


title: B1-mm_E-5

value: aVSMC

value: 10ug/L EGF


title: ChIPseq.AC7.BRD9.WT

description: genotype: wild type

value: wild type


title: ATACseq.BT549.ATAC.SMARCE1.WT.Rep1

description: lentivirus: full length SMARCE1


title: Xenopus_drug_ctrl_2

first: Megan

middle: M

last: Sperry

address: 3 Blackfan Circle

institute: Wyss Institute at Harvard University

description: Experiment 2: 1,4 DPCA treatment

hyb_protocol: Hybridization solutions were prepared by combining the fragmented, biotin-labeled cDNAs with hybridization cocktail (Affymetrix Hybridization, Wash, and Stain Kit). The mixtures were incubated in a thermal cycler at 99 °C for 2 min followed by 45 °C for 5 min. then loaded on Xenopus laevis Genome 2.0 arrays and incubated for 16-20 hours at 45 ºC and 60 rpm in an Affymetrix Hybridization Oven 645.

scan_protocol: Following hybridization, arrays were washed and stained on Affymetrix Fluidics Station 450s using the Affymetrix FS450_0001 protocol with the stains and buffers supplied in the Affymetrix Hybridization, Wash, and Stain Kit.  The stained arrays were scanned at 532 nm using an Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data were extracted from CEL files and Robust Multi-array Average (RMA) normalized in Matlab (Mathworks; Natick, MA) and output with linear scaling.

organism: Xenopus laevis

source_name: Xenopus, uninfected drug control

label_protocol: RNA samples were processed using a Nugen Ovation PICO WTA System V2 kit. The resulting cDNAs were purified using a Qiagen MinElute PCR Purification Kit following the modifications outlined in the Nugen protocol. The cDNAs were fragmented and labeled using a Nugen Encore Biotin Module.

growth_protocol: Xenopus laevis embryos were fertilized in vitro according to standard protocols in 0.1X Marc’s Modified Ringer’s solution (MMR; 10 mM Na+, 0.2 mM K+, 10.5 mM Cl–, 0.2 mM Ca2+, pH 7.8) and housed at 18°C. Since exclusively sterile filtered solutions, including MMR culture medium, were used to avoid confounding effects of seasonally-varying environmental bacteria, we dosed embryos overnight with 2.64 ul KoiZyme probiotic solution (Koi Care Kennel, Las Vegas, NV) per 1L of 0.1% MMR to avoid dysbiosis.

extract_protocol: For each experiment, RNA from each well containing 10 Xenopus embryos (n=2-3 replicates/condition) was separately extracted and purified using the RNeasy Micro Kit (Qiagen; Venlo, Netherlands).

treatment_protocol: Bacteria were streaked out from frozen glycerol stock of target bacterial strain on sheep blood agar media plates overnight at 37°C. A single colony was selected from the streak and grown in LB medium at 37°C. Exponentially growing bacteria were pelleted and resuspended in sterile saline/dextrose with 15% glycerol at a concentration of 1X109 CFU/ml. Faber-Nieuwkoop stage 13/14 embryos were injected with fresh bacterial suspensions using borosilicate glass needles calibrated for a bubble pressure of 25–30 kDa and 0.4 sec pulses to deliver 103–104 CFU of bacteria to each embryo. Bacterial injections of A. Hydrophila were performed with embryos submerged in 3% Ficoll prepared in 0.1X MMR. Prophylaxis and/or post-infection treatment of 40uM 1,4-DPCA was delivered to Xenopus and samples were collected 24h post-infection.

tag: infection

value: N

tag: treated post-infection

value: Y

tag: embryo prophylaxis

tag: pathogen prophylaxis


title: ChIPseq.AC7.ARID1A.WT

description: genotype: wild type

value: ChIP-seq


title: B1-mm_C-5

tag: cell type

value: Control


title: Sample.63.Beluga whale.202897220087_R03C01

tag: basename


title: Gr1_D7_T1_CD4

description: RNA of splenic CD3+ CD4+ T cells

tag: tissue

value: mouse spleen


title: ATACseq.BT549.ATAC.GFP.Rep2

description: lentivirus: full length GFP

tag: lentivirus

value: full-length GFP


title: Xenopus_drug_ctrl_3

description: Experiment 2: 1,4 DPCA treatment


title: Xenopus_drug_ctrl_1

description: Experiment 2: 1,4 DPCA treatment


title: Sample.66.Beluga whale.202897220087_R06C01

tag: species common name

tag: female

tag: canbeusedforagingstudies

value: yes


title: Xenopus_embryo-pathogen-prophylaxis_3

description: Experiment 2: 1,4 DPCA treatment

source_name: Xenopus, embryo & pathogen prophylaxis


title: Sample.62.Beluga whale.202897220087_R02C01


title: B1-mm_U-4

tag: mouse id used for cell isolation

tag: treatment type


title: Sample.64.Beluga whale.202897220087_R04C01


title: Sample.60.Beluga whale.202897220056_R06C02

value: no


title: ATACseq.BT549.ATAC.GFP.Rep1

description: lentivirus: full length GFP

tag: cell line


title: Sample.61.Beluga whale.202897220087_R01C01


title: Sample.59.Beluga whale.202897220056_R05C02


title: Xenopus_embryo-pathogen-prophylaxis_1

description: Experiment 2: 1,4 DPCA treatment


title: Xenopus_embryo-pathogen-prophylaxis_2

description: Experiment 2: 1,4 DPCA treatment


title: B1-mm_EU-4

tag: treatment length


title: ATACseq.AC7.ATAC.WT.Rep2

description: genotype: wild type

tag: genotype


title: B1-mm_E-4


title: Xenopus_pathogen-only-prophylaxis_3

description: Experiment 2: 1,4 DPCA treatment

source_name: Xenopus, pathogen-only prophylaxis


title: Sample.58.Beluga whale.202897220056_R04C02


title: Xenopus_pathogen-only-prophylaxis_2

description: Experiment 2: 1,4 DPCA treatment


title: ATACseq.AC7.ATAC.WT.DMSO.Rep2b

description: genotype: wild type_treatment: DMSO

tag: treatment

value: DMSO

tag: ngs approach


title: ATACseq.AC7.ATAC.WT.Rep1

description: genotype: wild type


title: B1-mm_U-3


title: Xenopus_pathogen-only-prophylaxis_1

description: Experiment 2: 1,4 DPCA treatment

tag: infection

tag: treated post-infection


title: B1-mm_C-4


title: ATACseq.AC7.ATAC.WT.DMSO.Rep2

description: genotype: wild type_treatment: DMSO


title: B1-mm_EU-3


title: ATACseq.AC7.ATAC.WT.DMSO.Rep1b

description: genotype: wild type_treatment: DMSO


title: B1-mm_E-3


title: ATACseq.AC7.ATAC.WT.DMSO.Rep1

description: genotype: wild type_treatment: DMSO


title: B1-mm_C-3


title: Sample.56.Beluga whale.202897220056_R02C02


title: Sample.55.Beluga whale.202897220056_R01C02


title: Xenopus_embryo-only-prophylaxis_3

description: Experiment 2: 1,4 DPCA treatment

source_name: Xenopus, embryo-only prophylaxis

tag: embryo prophylaxis

tag: pathogen prophylaxis


title: Sample.54.Beluga whale.202897220056_R06C01

tag: basename


title: Sample.57.Beluga whale.202897220056_R03C02


title: Xenopus_embryo-only-prophylaxis_2

description: Experiment 2: 1,4 DPCA treatment


title: Sample.53.Beluga whale.202897220056_R05C01


title: Xenopus_infected_untreated_3

description: Experiment 2: 1,4 DPCA treatment

source_name: Xenopus, infected & untreated


title: ATACseq.AC7.ATAC.WT.2uM.dBRDA.Rep2b

value: 2uM dBRD9A


title: Xenopus_embryo-only-prophylaxis_1

description: Experiment 2: 1,4 DPCA treatment


title: ATACseq.AC7.ATAC.WT.2uM.dBRDA.Rep1b


title: B1-mm_EU-2

source_name: Mouse aortic vascular smooth muscle cells

tag: cell type


title: ATACseq.AC7.ATAC.WT.100nM.CMP12.Rep2b

value: 100nM CMP12


title: Sample.52.Beluga whale.202897220056_R04C01

value: Beluga whale


title: B1-mm_U-2


title: B1-mm_E-2


title: ATACseq.AC7.ATAC.WT.100nM.CMP12.Rep1b


title: B1-mm_C-2


title: B1-mm_U-1


title: ATACseq.AC7.ATAC.SMARCE1_KO.DMSO.Rep2b

description: genotype: SMARCE1 null_treatment: DMSO

value: SMARCE1 null


title: ATACseq.AC7.ATAC.SMARCE1_KO.DMSO.Rep2

description: genotype: SMARCE1 null_treatment: DMSO

value: ATAC-seq


title: Xenopus_embryo-pathogen-prophylaxis_post-treat_3

description: Experiment 2: 1,4 DPCA treatment

source_name: Xenopus, embryo & pathogen prophylaxis & post-infection treatment


title: Sample.50.Beluga whale.202897220056_R02C01


title: B1-mm_EU-1

value: aVSMC


title: Xenopus_embryo-pathogen-prophylaxis_post-treat_1

description: Experiment 2: 1,4 DPCA treatment


title: Xenopus_embryo-pathogen-prophylaxis_post-treat_2

description: Experiment 2: 1,4 DPCA treatment


title: Sample.51.Beluga whale.202897220056_R03C01


title: Xenopus_infected_untreated_2

description: Experiment 2: 1,4 DPCA treatment


title: Xenopus_infected_untreated_1

description: Experiment 2: 1,4 DPCA treatment


title: Sample.47.Beluga whale.202897220054_R05C02


title: Sample.46.Beluga whale.202897220054_R04C02


title: B1-mm_E-1

value: 10ug/L EGF


title: ATACseq.AC7.ATAC.SMARCE1_KO.DMSO.Rep1

description: genotype: SMARCE1 null_treatment: DMSO


title: Xenopus_embryo-only-prophylaxis_post-treat_2

description: Experiment 2: 1,4 DPCA treatment

source_name: Xenopus, embryo-only prophylaxis & post-infection treatment


title: B1-mm_C-1


title: ATACseq.AC7.ATAC.SMARCE1_KO.DMSO.Rep1b

description: genotype: SMARCE1 null_treatment: DMSO


title: Sample.49.Beluga whale.202897220056_R01C01


title: ATACseq.AC7.ATAC.SMARCE1_KO.2uM.dBRDA.Rep2b


title: Gr4_D7_TM3_CD8

description: RNA of splenic CD3+ CD8+ T cells

tag: tissue


title: m189

value: 10ug/L EGF + 10nM AngII + 1uM U46619


title: Sample.48.Beluga whale.202897220054_R06C02

tag: species common name


title: m188


title: ATACseq.AC7.ATAC.SMARCE1_KO.100nM.CMP12.Rep2b


title: ATACseq.AC7.ATAC.SMARCE1_KO.2uM.dBRDA.Rep1b


title: Xenopus_embryo-only-prophylaxis_post-treat_1

description: Experiment 2: 1,4 DPCA treatment

value: N


title: Sample.43.Beluga whale.202897220054_R01C02

tag: female


title: m187

value: 10ug/L EGF + 10nM AngII


title: Gr7_D14_T1_CD8

description: RNA of splenic CD3+ CD8+ T cells

source_name: Mouse CD3+ CD8+ T cells from spleen 14 days after TxT without MDSC treatment


title: Xenopus_post-treat_only_2

description: Experiment 2: 1,4 DPCA treatment

source_name: Xenopus, post-infection treatment only

value: Y


title: Xenopus_embryo-only-prophylaxis_post-treat_3

description: Experiment 2: 1,4 DPCA treatment


title: Sample.44.Beluga whale.202897220054_R02C02

tag: canbeusedforagingstudies


title: Sample.45.Beluga whale.202897220054_R03C02


title: Xenopus_post-treat_only_3

description: Experiment 2: 1,4 DPCA treatment


title: Xenopus_post-treat_only_1

description: Experiment 2: 1,4 DPCA treatment


title: Xenopus_neg_ctrl_3

description: Experiment 2: 1,4 DPCA treatment

source_name: Xenopus, uninfected negative control


title: Sample.41.Beluga whale.202897220054_R05C01


title: m186

tag: mouse id used for cell isolation


title: ATACseq.AC7.ATAC.SMARCE1_KO.100nM.CMP12.Rep1b


title: Sample.42.Beluga whale.202897220054_R06C01


title: m185

tag: treatment type

value: 10nM AngII


title: ATACseq.AC7.ATAC.SMARCE1_KO.Rep2

description: genotype: SMARCE1 null

tag: cell line


title: ATACseq.AC7.ATAC.SMARCE1_KO.Rep1

description: genotype: SMARCE1 null


title: m184

tag: treatment length


title: MCF_7_siCtrl_E2_45_min_Rep_2_Input_R1

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
ChIP-seq: aligned to hg38 human reference genome using bwa.
Mapped reads were sorted and captured in bam files for futher downstream analyses of transcript assembly and transcription start site calling.
bigWig were generated for browser tracks using BEDtools.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: MCF-7 cells were grown in phenol red-free minimal essential medium supplemented with 5% charcoal-dextran treated calf serum, 2 mM GlutaMAX, 100U/mL penicillin-streptomycin, 25 ug/mL gentamicin.

extract_protocol:
Cells were treated, cross-linked with 1% formadelhyde, quenched with 125 mM glycine, and harvested in PBS.  Crude chromatin fraction was then sheared by a Bioruptor sonicator (Diagenode) for 30 cycles (30 sec on, 30 sec off).  Fragment size was verified using agarose gel before 500 micrograms of chromatin was used for immunoprecipitation using 2 microgram of anti-ERalpha antibody (Millipore Sigma, 06-935).  Sample was then washed, and DNA decrosslinked before library preparation.
ChIP'ed DNA by an antibody against estrogen receptor alpha (Millipore Sigma, #06-935), and was used to generate ChIP-seq libraries.  The final libraries were quantified and subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina HiSeq 2000. Libraries were sequenced using an Illumina HiSeq 2000.

treatment_protocol: Cells were transfected with siRNA against BCAS2 for 48 hrs before 40 min treatment with DMSO or 100 nM 17-b-estradiol.

value: Breast cancer cells

value: 100 nM 17-b-estradiol

tag: transfection

value: siCtrl


title: Sample.39.Beluga whale.202897220054_R03C01

value: yes


title: m183

value: Control


title: Xenopus_neg_ctrl_2

description: Experiment 2: 1,4 DPCA treatment


title: MCF_7_siCtrl_E2_45_min_Rep_1_Input_R1

tag: treatment


title: Xenopus_neg_ctrl_1

description: Experiment 2: 1,4 DPCA treatment


title: m181


title: MCF_7_siCtrl_E2_45_min_Rep_2_ER_ChIP_R1


title: m180


title: m179


title: MCF_7_siCtrl_E2_0_Rep_2_Input_R1

value: DMSO


title: m182


title: MCF_7_siCtrl_E2_0_Rep_1_Input_R1


title: m178


title: Xenopus_Kpneumoniae_28h_2

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with Kpneumoniae, 28h

treatment_protocol: Bacteria were streaked out from frozen glycerol stock of target bacterial strain on sheep blood agar media plates overnight at 37°C. A single colony was selected from the streak and grown in LB medium at 37°C. Exponentially growing bacteria were pelleted and resuspended in sterile saline/dextrose with 15% glycerol at a concentration of 1X109 CFU/ml. Faber-Nieuwkoop stage 13/14 embryos were injected with fresh bacterial suspensions using borosilicate glass needles calibrated for a bubble pressure of 25–30 kDa and 0.4 sec pulses to deliver 103–104 CFU of bacteria to each embryo. Bacterial injections were performed with embryos submerged in 3% Ficoll prepared in 0.1X MMR.

value: K. pneumoniae

tag: exposure time


title: Sample.38.Beluga whale.202897220054_R02C01

value: Beluga whale


title: Sample.40.Beluga whale.202897220054_R04C01


title: Xenopus_Kpneumoniae_28h_1

description: Experiment 1: Pathogen screening

tag: infection


title: MCF_7_siCtrl_E2_45_min_Rep_1_ER_ChIP_R1


title: Xenopus_Kpneumoniae_28h_3

description: Experiment 1: Pathogen screening


title: MCF_7_siCtrl_E2_0_Rep_2_ER_ChIP_R1


title: Sample.35.Beluga whale.202897220052_R05C02


title: Sample.37.Beluga whale.202897220054_R01C01


title: Xenopus_Spneumoniae_28h_3

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with Spneumoniae, 28h

value: S. pneumoniae


title: Sample.34.Beluga whale.202897220052_R04C02


title: Xenopus_Spneumoniae_28h_1

description: Experiment 1: Pathogen screening


title: Xenopus_Ahydrophila_28h_3

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with A. hydrophila, 28h

value: A. hydrophila


title: MCF_7_siCtrl_E2_0_Rep_1_ER_ChIP_R1


title: Sample.36.Beluga whale.202897220052_R06C02

source_name: Skin


title: Xenopus_Spneumoniae_28h_2

description: Experiment 1: Pathogen screening


title: Sample.32.Beluga whale.202897220052_R02C02


title: m176

value: aVSMC


title: Xenopus_Ahydrophila_28h_2

description: Experiment 1: Pathogen screening


title: Sample.31.Beluga whale.202897220052_R01C02


title: MCF_7_siBCAS2_E2_45_min_Rep_2_Input_R1

value: siBCAS2 #563


title: Sample.30.Beluga whale.202897220052_R06C01


title: m175

value: 10ug/L EGF + 10nM AngII + 1uM U46619


title: Xenopus_Ahydrophila_28h_1

description: Experiment 1: Pathogen screening


title: Sample.33.Beluga whale.202897220052_R03C02


title: m174


title: m177

value: 10ug/L EGF


title: Sample.29.Beluga whale.202897220052_R05C01


title: MCF_7_siBCAS2_E2_45_min_Rep_1_Input_R1


title: m173

value: 10ug/L EGF + 10nM AngII


title: MCF_7_siBCAS2_E2_45_min_Rep_2_ER_ChIP_R1


title: MCF_7_siBCAS2_E2_0_Rep_2_Input_R1


title: m171


title: m170


title: m172


title: MCF_7_siBCAS2_E2_0_Rep_1_Input_R1


title: Xenopus_Abaumannii_28h_2

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with A. baumannii, 28h

value: A. baumannii


title: Sample.26.Beluga whale.202897220052_R02C01


title: Xenopus_Abaumannii_28h_1

description: Experiment 1: Pathogen screening


title: Sample.28.Beluga whale.202897220052_R04C01


title: Sample.27.Beluga whale.202897220052_R03C01


title: Xenopus_Abaumannii_28h_3

description: Experiment 1: Pathogen screening


title: MCF_7_siBCAS2_E2_0_Rep_2_ER_ChIP_R1


title: Xenopus_Paeruginosa_28h_3

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with P. aeruginosa, 28h

value: P. aeruginosa


title: Xenopus_Paeruginosa_28h_1

description: Experiment 1: Pathogen screening


title: MCF_7_siBCAS2_E2_0_Rep_1_ER_ChIP_R1

value: Breast cancer cells


title: m169


title: m168


title: MCF_7_siCtrl_E2_6_hr_Rep_2_R1

data_processing:
RNA-seq: aligned to hg38 human reference genome using Star.
Mapped reads were sorted and captured in bam files for futher downstream analyses of differential expressed genes using DESeq2.
bigWig were generated for browser tracks using BEDtools.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
RNA-seq: used DNAaway RNA mini-prep kit (Bio Basic, BS88136).
RNA-seq: RNA was enriched with oligo-dT beads to generate RNA-seq libraries. The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina HiSeq 2000. Libraries were sequenced using an Illumina HiSeq 2000.

treatment_protocol: Cells were transfected with siRNA against BCAS2 for 48 hrs before 6 hr treatment with DMSO or 100 nM 17-b-estradiol.

value: 100 nM 17-b-estradiol

tag: time

value: 6 hr


title: MCF_7_siBCAS2_E2_45_min_Rep_1_ER_ChIP_R1


title: m167


title: Sample.25.Beluga whale.202897220052_R01C01

value: yes


title: Xenopus_Saureus_28h_3

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with S. aureus, 28h

value: S. aureus


title: MCF_7_siCtrl_E2_6_hr_Rep_1_R1

value: siCtrl


title: m166


title: MCF_7_siCtrl_E2_0_hr_Rep_2_R1

value: 0 hr


title: MCF_7_siCtrl_E2_0_hr_Rep_2_R1_Reseq


title: m164

value: 10nM AngII


title: Xenopus_Paeruginosa_28h_2

description: Experiment 1: Pathogen screening


title: Xenopus_Saureus_28h_2

description: Experiment 1: Pathogen screening


title: MCF_7_siCtrl_E2_0_hr_Rep_1_R1.


title: Sample.23.Beluga whale.202897220042_R05C02

value: Beluga whale


title: Sample.21.Beluga whale.202897220042_R03C02


title: Sample.20.Beluga whale.202897220042_R02C02


title: Sample.24.Beluga whale.202897220042_R06C02


title: Xenopus_Saureus_28h_1

description: Experiment 1: Pathogen screening


title: Xenopus_control_28h_2

description: Experiment 1: Pathogen screening

source_name: Xenopus, control, 28h

value: control


title: Sample.19.Beluga whale.202897220042_R01C02


title: Sample.18.Beluga whale.202897220042_R06C01


title: m163

value: aVSMC


title: m162

value: Control


title: Sample.22.Beluga whale.202897220042_R04C02


title: m161

value: 10ug/L EGF + 10nM AngII + 1uM U46619


title: m165


title: MCF_7_siBCAS2_563_E2_6_hr_Rep_2_R1

value: siBCAS2 #563


title: MCF_7_siBCAS2_563_E2_6_hr_Rep_1_R1.


title: Xenopus_Kpneumoniae_4h_2

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with K. pneumoniae, 4h

value: K. pneumoniae


title: Xenopus_Kpneumoniae_4h_1

description: Experiment 1: Pathogen screening


title: Sample.15.Beluga whale.202897220042_R03C01


title: m160


title: Xenopus_Spneumoniae_4h_3

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with S. pneumoniae, 4h

value: S. pneumoniae


title: Xenopus_Kpneumoniae_4h_3

description: Experiment 1: Pathogen screening


title: Xenopus_control_28h_1

description: Experiment 1: Pathogen screening


title: MCF_7_siCtrl_E2_0_hr_Rep_1_R1_Reseq


title: m159

value: 10ug/L EGF + 10nM AngII


title: MCF_7_siBCAS2_563_E2_0_hr_Rep_1_R1

value: Breast cancer cells


title: MCF_7_siBCAS2_562_E2_6_hr_Rep_2_R1

value: 100 nM 17-b-estradiol

value: siBCAS2 #562


title: m157


title: Sample.17.Beluga whale.202897220042_R05C01

value: yes


title: m158


title: Sample.14.Beluga whale.202897220042_R02C01


title: Sample.13.Beluga whale.202897220042_R01C01


title: Sample.16.Beluga whale.202897220042_R04C01


title: Xenopus_Spneumoniae_4h_2

description: Experiment 1: Pathogen screening


title: Xenopus_Spneumoniae_4h_1

description: Experiment 1: Pathogen screening


title: m156

value: 10ug/L EGF


title: MCF_7_siBCAS2_563_E2_0_hr_Rep_2_R1


title: MCF_7_siBCAS2_562_E2_6_hr_Rep_1_R1_Reseq

value: 6 hr


title: MCF_7_siBCAS2_562_E2_6_hr_Rep_1_R1


title: m155


title: Sample.11.Beluga whale.202894750042_R05C02


title: Sample.12.Beluga whale.202894750042_R06C02


title: Xenopus_Ahydrophila_4h_2

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with A. hydrophila, 4h

value: A. hydrophila


title: m154

source_name: Mouse aortic vascular smooth muscle cells


title: Xenopus_Ahydrophila_4h_3

description: Experiment 1: Pathogen screening


title: Sample.10.Beluga whale.202894750042_R04C02


title: MCF_7_siBCAS2_562_E2_0_hr_Rep_2_R1

value: 0 hr


title: MCF_7_siBCAS2_562_E2_0_hr_Rep_1_R1


title: m153


title: m152


title: MCF_7_siBCAS2_562_E2_0_hr_Rep_1_R1_Reseq


title: m151


title: m150

value: 10nM AngII


title: MCF7_E2_MinusRibo_PlusPolyA_Rep2

description:
PolyA-enriched RNA
Replicates merged

data_processing:
RNA-seq: aligned to hg38 human reference genome using Star.
Mapped reads were sorted and captured in bam files for futher downstream analyses of transcript assembly and transcription start site calling.
bigWig were generated for browser tracks using BEDtools.
Genome_build: hg38

source_name: MCF-7 breast cancer cells

extract_protocol:
RNA-seq: used DNAaway RNA mini-prep kit (Bio Basic, BS88136).
RNA-seq: rRNA was depleted followed by polyA enrichment RNA using Dynabeads Oligo(dT)25 (Invitrogen).  Both polyA-enriched and -depleted fractions were then used to generate RNA-seq libraries. The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina HiSeq 2000. Libraries were sequenced using an Illumina HiSeq 2000.

treatment_protocol: 45 min with DMSO or 100 nM 17-b-estradiol.


title: MCF7_E2_MinusRibo_PlusPolyA_Rep1

description:
PolyA-enriched RNA
Replicates merged


title: Sample.9.Beluga whale.202894750042_R03C02

value: Beluga whale


title: Xenopus_Abaumannii_4h_2

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with A. baumannii, 4h

value: A. baumannii


title: m149

value: aVSMC


title: MCF7_E2_MinusRibo_MinusPolyA_Rep2_Reseq

description:
PolyA-depleted RNA
Replicates merged


title: MCF7_E2_MinusRibo_MinusPolyA_Rep2

description:
PolyA-depleted RNA
Replicates merged


title: Xenopus_Abaumannii_4h_3

description: Experiment 1: Pathogen screening


title: Xenopus_Ahydrophila_4h_1

description: Experiment 1: Pathogen screening


title: m148

value: Control


title: Sample.8.Beluga whale.202894750042_R02C02


title: Sample.7.Beluga whale.202894750042_R01C02


title: Sample.5.Beluga whale.202894750042_R05C01


title: Sample.4.Beluga whale.202894750042_R04C01


title: Xenopus_Paeruginosa_4h_2

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with P. aeruginosa, 4h

value: P. aeruginosa


title: MCF7_E2_MinusRibo_MinusPolyA_Rep1_Reseq

description:
PolyA-depleted RNA
Replicates merged


title: Xenopus_Abaumannii_4h_1

description: Experiment 1: Pathogen screening


title: Sample.6.Beluga whale.202894750042_R06C01


title: nhr-178(gk1005)_0.3_µM_Antimycin_Replicate_3

city: Worcteser

first: SUSHILA

last: BHATTACHARYA

address: Albert Sherman Center, Room 5.1051 386 Plantation St.

department: Department of Systems Biology (DSB)

institute: UMass Chan Medical School

data_processing:
BGI internal software "SOAPnuke" was used to remove adaptors and low quality reads with parameters: -n 0.001 -l 20 -q 0.4 -A 0.25. Low quality reads are defined as having greater than 40% bases whose quality is less than 20.
Reads were aligned to the reference genome using Bowtie2 with default parameters.
RSEM was used for estimation of read counts with default parameters
The Deseq2 package in R 3.6.3 was used for differential expression analysis.
Assembly: c_elegans.PRJNA13758 (WormBase WS271)
Supplementary files format and content: tab dilimeted file containing TPM matrix for all samples and all genes

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were maintained on NGM-agar on an E. coli OP50 diet prior to experiment. They were synchronized by an 18 hour L1 arrest post-buffered bleach treatment.

extract_protocol:
A minumum of 1000 staged animals were collected and washed thrice in M9 bufferRNA was extracted from early adult stage animals and purified using Direct-zol RNA Miniprep Kit (Zymo Research) R2050)
BGI standard protocol

treatment_protocol: Synchronized L1 animals were grown on NGM-agar- 0.3µM Antimycin A in DMSO E. coli HT115 with DMSO E. coli HT115 as control

tag: strain

value: Mutant

tag: genotype

tag: Stage

value: Adult

value: grown on NGM + 0.3µM Antimycin + E. coli HT115


title: Xenopus_Paeruginosa_4h_3

description: Experiment 1: Pathogen screening


title: Sample.3.Beluga whale.202894750042_R03C01

tag: basename


title: Xenopus_Paeruginosa_4h_1

description: Experiment 1: Pathogen screening


title: nhr-178(gk1005)_0.3_µM_Antimycin_Replicate_2

value: grown on NGM + 0.3µM Antimycin+ E. coli HT115


title: Xenopus_Saureus_4h_3

description: Experiment 1: Pathogen screening

source_name: Xenopus, infected with S. aureus, 4h

value: S. aureus


title: MCF7_E2_MinusRibo_MinusPolyA_Rep1

description:
PolyA-depleted RNA
Replicates merged

tag: cell type

value: Breast cancer cells

value: 100 nM 17-b-estradiol


title: Sample.2.Beluga whale.202894750042_R02C01

tag: species common name

value: yes


title: Xenopus_Saureus_4h_2

description: Experiment 1: Pathogen screening


title: XEGs replicate 2

city: Leiden

first: Stefan

last: Semrau

state: Zuid-Holland

address: Einsteinweg 55

department: Physics

institute: Leiden University

description: Contains E14 mESC CITE-seq spike-ins (CD15 antibody) and XEN-eGFP CITE-seq spike-ins (CD140 antibody)

data_processing:
Single-cell expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
Counts were normalized with the scran package in R
Cell types were assigned by vote of the K-nearest-neighbors from the Pijuan-Sala dataset (GSE87038)
Genome_build: mm10 with mCherry and eGFP
CITE in the name indicates CITE-seq library preparation
Supplementary_files_format_and_content: fq.gz: compressed raw fastq file from illumina sequencing (CITE in the name indicates CITE-seq library preparation); matrix.mtx.gz:compressed matrix of UMI counts where cells are columns and genes rows; barcodes.tsv: compressed list of 16bp barcodes corresponding to the columns of matrix; features.fq.gz: compressed list of HUGO and ensembl identifiers corresponding to the rows of matrix; normCounts.tsv: Compressed table of normalized expression and cell type assignments.

source_name: Cell culture

growth_protocol: Growth protocol P3 with chiron as described in van den Brink et al (2014) in Development. Differences: Gastruloids start with 200 E14 mouse embryonic stem cells (mESCs), PEGs start with a mixture 150 E14 mESCs and 50 Extra-embryonic-endoderm-like (XEN) cells and cells are collected after 4 days.

extract_protocol:
Organoids were pooled and disociated with TrypLE. Spike-ins (see sample descriptions) were added before proceeding with single-cell RNA sequencing library preparation.
10X library: 10x RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 3 Chemistry (10x Genomics) according to the manufacturer's protocol. CITE-seq libraries: CITE-seq libraries were prepared according to the CITE-seq protocol from New York Genome Center version 2019-02-13. Sequencing: Libraries were sequenced on an Illumina Novaseq6000 at 150bp paired end.
Paired end RNA-seq

treatment_protocol: No treatment

tag: starting cells

value: mouse ES cells, XEN-eGFP cells


title: Xenopus_Saureus_4h_1

description: Experiment 1: Pathogen screening


title: Sample.1.Beluga whale.202894750042_R01C01

tag: female

tag: canbeusedforagingstudies


title: nhr-178(gk1005)_0.3_µM_Antimycin_Replicate_1

value: grown on NGM + 0.3µMAntimycin + E. coli HT115


title: XEGs replicate 1

description: Contains E14 mESC CITE-seq spike-ins (CD15 antibody)

value: mouse ES cells, XEN cells


title: Gastruloids (CITE_seq) replicate 2

description:
Contains mCherry-GPI mESC spike-ins
gastruloids_rep2_barcodes.tsv
gastruloids_rep2_features.tsv
gastruloids_rep2_matrix.mtx.gz
gastruloids_rep2_normCounts.tsv

growth_protocol: Growth protocol P3 with chiron as described in van den Brink et al (2014) in Development. Differences: Gastruloids start with 200 E14 mouse embryonic stem cells (mESCs), neuroloids start with a mixture 150 E14 mESCs and 50 Extra-embryonic-endoderm-like (XEN) cells and cells are collected after 4 days.

value: mouse ES cells


title: MCF7_Veh_PlusTAP_Rep1

description:
Capped-enriched RNA
Replicates merged

data_processing:
Library strategy: PRO-cap
PRO-cap: aligned to hg38 human reference genome using bwa.
Mapped reads were sorted and captured in bam files for futher downstream analyses of transcript assembly and transcription start site calling.
bigWig were generated for browser tracks using BEDtools.
Genome_build: hg38

extract_protocol:
PRO-cap: isolated nuclei before performing nuclear run-on with biotinylated nucleotides.
PRO-cap: followed the protocol of Mahat et al, 2016 Nat Protoc.  Libraries were sequenced using an Illumina HiSeq 2000.

value: DMSO


title: nhr-45(tm1307)_0.3_µM_Antimycin_Replicate_3


title: XEGs (CITE_Seq) replicate 2

description:
Contains E14 mESC CITE-seq spike-ins (CD15 antibody) and XEN-eGFP CITE-seq spike-ins (CD140 antibody)
PEGs_rep2_barcodes.tsv
PEGs_rep2_features.tsv
PEGs_rep2_matrix.mtx.gz
PEGs_rep2_normCounts.tsv


title: MCF7_Veh_MinusTAP_Rep2

description:
Capped-enriched RNA
Replicates merged


title: Gastruloids replicate2

description: Contains mCherry-GPI mESC spike-ins


title: nhr-45(tm1307)_0.3_µM_Antimycin_Replicate_2


title: Xenopus_control_4h_1

description: Experiment 1: Pathogen screening

source_name: Xenopus, control, 4h

value: control


title: MCF7_Veh_MinusTAP_Rep1

description:
Capped-enriched RNA
Replicates merged


title: nhr-45(tm1307)_0.3_µM_Antimycin_Replicate_1


title: Gastruloids replicate1

description: Contains mCherry-GPI mESC spike-ins


title: +Asn input DNA

city: Indianapolis

first: Ji

last: Zhang

state: IN

address: 1044 W Walnut Street, R4-170

department: Pediatrics

institute: Indiana University

data_processing:
Base calling and quality scoring were performed in Illumina NovaSeq 6000
The reads were mapped to the human genome (UCSC hg38) using Bowtie2 (v2.4.4), PICARD (v2.18.26) function MarkDuplicates was used to identify duplicate reads
MACS2 (v 2.2.7.1) were used to call peaks using Input as control at FDR cut off of less than 1e-2
The signal at each base was normalized by per 10 million reads
Assembly: hg38
Supplementary files format and content: Bigwig file showing the normalized read signal, merged peak file

growth_protocol: RS4;11 cells were cultured in each condition for 24 hours. Around 10 million cells were used per collection.

extract_protocol:
For H3K4me3 ChIP-seq, we used the Covaris truChIP Chromatin Shearing Reagent Kit; for RNA-seq, we used Trizol for whole cell RNA extraction.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ferric Nitrate was added at 10 µM in the presence of 0.75 µM Hinokitiol

value: complete medium

tag: chip antibody

value: none (input)


title: -Asn input DNA

tag: cell line

value: asparagine-free medium


title: -Asn+Fe H3K4me3 rep3

value: asparagine-free medium plus ferric nitrate


title: -Asn+Fe input DNA


title: MCF7_E2_PlusTAP_Rep2

description:
Capped-enriched RNA
Replicates merged


title: MCF7_Veh_PlusTAP_Rep2

description:
Capped-enriched RNA
Replicates merged


title: -Asn+Fe H3K4me3 rep2


title: Wild_Type_0.3_µM_Antimycin_Replicate_3

value: Wild-type

value: Adult


title: MCF7_E2_MinusTAP_Rep2

description:
Capped-enriched RNA
Replicates merged


title: MCF7_E2_PlusTAP_Rep1

description:
Capped-enriched RNA
Replicates merged


title: -Asn+Fe H3K4me3 rep1


title: Xenopus_control_4h_2

description: Experiment 1: Pathogen screening


title: Q3.4D3

city: London,

first: Khaleda Afrin

last: Bari

state: ON

address: 1151 Richmond St

department: Anatomy and Cell Biology

country: Canada

institute: Western University

data_processing:
Sequence reads were obtained from Genewiz (South Plainfield, NJ)
Sequenced reads were trimmed for adaptor sequence and then mapped to S. cerevisiae whole genome using STAR v2.5.4b
Raw counts for each sample were obtained using featureCounts v1.6.0
Differentially expressed genes were determined using DESeq2 v1.26.0
Assembly: Saccharomyces cerevisiae S288C reference genome (assembly R64-2-1)
Supplementary files format and content: Raw gene counts table for every gene and every sample
Supplementary files format and content: Normalized counts text files for each gene for each sample

organism: Saccharomyces cerevisiae

growth_protocol: Strains were grown to mid-log phase in synthetic complete media

extract_protocol:
RNA was extracted using the MasterPure Yeast RNA purification kit (Lucigen) according to the manufacturer’s instructions.
Stranded Illumina TruSeq cDNA libraries with poly dT enrichment were prepared from high quality total RNA (RIN > 8)

value: Mutant

value: MATa ade2-1 can1-100 trp1-1 leu2-3 his3-11 ura3-1


title: -Asn H3K4me3 rep3


title: WT.3D3

value: WT


title: MCF7_E2_MinusTap_Rep1

description:
Capped-enriched RNA
Replicates merged

value: Breast cancer cells

value: 100 nM 17-b-estradiol


title: nhr-178(gk1005)_DMSO_Replicate_3

value: grown on NGM + DMSO + E. coli HT115


title: -Asn H3K4me3 rep2


title: WT.2D3


title: Pou2f3.mTEC.rep#8

description: CUT&Tag

source_name: Thymus

value: mTEC


title: nhr-178(gk1005)_DMSO_Replicate_2


title: Q3.3D3


title: WT.1D3


title: nhr-45(tm1307)_DMSO_Replicate_3


title: Wild_Type_0.3_µM_Antimycin_Replicate_2

value: grown on NGM + 0.3µM Antimycin+ E. coli HT115


title: nhr-178(gk1005)_DMSO_Replicate_1


title: Q3.3D0


title: +Asn H3K4me3 rep3


title: Pou2f3.mTEC.rep#6

description: CUT&Tag


title: Pou2f3.mTEC.rep#5

description: CUT&Tag


title: Pou2f3.mTEC.rep#4

description: CUT&Tag


title: +Asn H3K4me3 rep1


title: Q3.1D0


title: Q3.2D0


title: Wild_Type_0.3_µM_Antimycin_Replicate_1

value: grown on NGM + 0.3µMAntimycin + E. coli HT115


title: Q3.2D3


title: Human-Kidney-snATAC-seq Sample 4, snATAC-seq

city: Philadelphia

first: Hongbo

last: Liu

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: 10x single-cell ATAC-seq kit

data_processing:
After quality control, the library was sequenced on an Illumina NovaSeq 6000 paired-end kits. We integarated this new datasets (four samples) and our previous datasets (two samples, GSE172008) and obtaiend the open chromatin information of 61,440 high quality cells. Reads were aligned to human genome (hg19) with SnapATAC (v2.0). After quality control and peak calling, a cell-gene activity score matrix was built by integrating all fragments overlapping with gene transcripts (in GENCODE v19 annotations). Cluster annotation was performed using a published list of cell-type marker genes, and 13 main clusters were identified (Proximal tubule segment 1, Proximal tubule segment 2, Proximal tubule segment 3, Loop of Henle, Distal convoluted tubule, Collecting duct principal cell, Collecting duct intercalated cell, Podocyte, Endothelial, Stroma, Immune, Lymph cell and injured proximal tubule). The injured proximal tubule cells were not included in further analysis due to its potential disease status. For each of remained 12 clusters (57,229 cells), we identified cell type-specific differentially accessible regions (DARs) by one-sided Fisher’s exact test between a given cell type and each of the other cell types for each of 410,994 peaks. Peaks with FDR < 0.05 and fold change > 1 in at least half of pairwise comparisons were defined as cell type specific DARs, thus allowing inclusion of DARs shared by closely related cell types (the three segments of proximal tubules).
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

growth_protocol: Human kidney samples were obtained from the non-tumor tissue of partial or radical nephrectomy patients from the Hospital of the University of Pennsylvania

extract_protocol:
Kidneys were minced and lysed in 2 mL lysis buffer for 15 min. Tissue lysis reaction was then blocked by adding 10 mL 1x PBS into each tube, and solution was passed through a 40 μm cell strainer. Cell debris and cytoplasmic contaminants were removed by Nuclei PURE Prep Nuclei Isolation Kit (Sigma, NUC-201) after centrifugation at 13,000 RPM for 45 min.  Libraries were prepared according to 10x Genomics's instructions (CG000209) accompanying the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1.  Single nuclei ATAC-seq
Single nucleus ATAC-seq libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit according to manufacturer’s manual.

tag: tissue

value: Kidney

tag: gender

value: Female

tag: age

value: 65 years old

tag: race

value: White


title: Human-Kidney-snATAC-seq Sample 3, snATAC-seq

description: 10x single-cell ATAC-seq kit

value: Male

value: 74 years old

value: African American