title: 52h_Multiome

data_processing:
Reference and Quantification: Alignment, processing, and counting of both ATAC and RNA molecules were performed using Cell Ranger ARC. The mouse mm10 genome was used a reference. For the scATAC-seq data, gene annotations were extracted from EnsDb.Mmusculus.v79.
Quality control and filtering: . Cells from the 48 h and 52 h samples were filtered using total counts from both RNA and ATAC-seq datasets; cells that had greater than 1000 ATAC-seq counts/cells and 1000 transcript counts/cell were kept, resulting in a dataset of 1317 cells from the 48 h sample and a dataset of 1096 cells from the 52 h sample. The scATAC-seq data was normalized by performing term frequency-inverse document frequency (TF-IDF) normalization105. For the scRNA-seq data SCTransform-based normalization was performed in Seurat
Assembly: GRCm38 primary assembly
Library strategy: Mulitome (RNA-seq and ATAC-seq)

molecule: other

extract_protocol:
Briefly, 300 mESC were plated in 40 µl N2B27 into ultra-low attachment, round-bottom 96-well plates (7007, Corning). After 48 h, 150 ml of N2B27 supplemented with 3 µM Chir were added to each well. Gastruloids were collected at 48 h (384 gastruloids) and 52 h (288 gastruloids) were collected. Gastruloids were transferred into a tube, spun and medium was removed. Gastruloids were dissociated by incubating with Accutase for 4 min at 37°C with intermediate mechanical dissociation. After spinning with DMEM/F-12 with 0.1% BSA, cells were resuspended in Freezing medium (90% Serum medium, 10% DMSO (Sigma, 276855)), cell concentration was determined and 180,000 cells per vial were frozen and stored at -80°C for later continuation of the sample preparation. After thawing, cells were resuspended in PBS 0.8% BSA and washed twice in PBS 0.04% BSA. Cells were then resuspended in Lysis Buffer containing 10 mM Tris-HCl, pH 7.4 (Sigma-Aldrich, T2194), 10 mM Sodium Chloride (Sigma-Aldrich, 59222C), 3 mM Magnesium Chloride (Sigma-Aldrich, M1028), 0.01% Tween-20 (Bio-Rad, 1662404), 0.01% NP40 Substitute (Sigma-Aldrich, 74385), 0.005% Digitonin (Sigma-Aldrich D141-100MG), 1% BSA (Miltenyi Biotec, 130-091-376), 1 mM DTT (Sigma-Aldrich, 646563), Protector RNase inhibitor (Sigma-Aldrich 3335402001) and nuclease-free water (Ambion, AM9937). The suspension was incubated for 5 min on ice. The reaction was stopped with Wash Buffer (10 mM Tris-HCl, pH 7.4, 10 mM Sodium Chloride, 3 mM Magnesium Chloride, 1% BSA, 0.1% Tween-20, 1 mM DTT, 1 U/µl RNase inhibitor, and nuclease-free water) and span down for 5 min at 500g at 4°C. The pellet was resuspended in Wash buffer and again span down for 5 min at 500g at 4°C. The pellet was resuspended in 1X Diluted Nuclei Buffer consisting of 1X Nuclei Buffer (stock of 20X, 10x Genomics, 2000207), 1 mM DTT, 1 U/µl RNase inhibitor and nuclease-free water and nuclei concentration was determined. Nuclei were span down for 5 min at 500g at 4°C and resuspended in the respective volume of 1X Diluted Nuclei Buffer according to the 10x Multiome user guide for theoretically targeting 5,000 nuclei.
Single cell Multiome experiments were performed using the 10x Chromium Single Cell Multiome ATAC + Gene Expression (GEX) kit (1000283) following manufacturer’s instructions.    Briefly, nuclei suspensions were incubated in a transposition mix where open chromatin DNA was preferentially fragmented and adapter sequences were added to the ends of the DNA fragments.    Afterwards, nuclei were mixed with reverse transcription mix, and gel beads and oil were loaded onto a 10x microfluidic chip to be co-encapsulated into nanodroplets, forming GEMs. Inside each GEM containing a nucleus, for GEX, first strand cDNA synthesis occurred, where each mRNA was tagged with a UMI and a barcode unique for each nucleus and a 30nt poly (dT). In the same partition, for ATAC, transposed DNA was tagged with P5 adaptor followed by 16nt barcode and a spacer. Subsequently, the reaction was quenched. The droplets were broken, pooled fractions recovered and purified using Dynabeads MyOne Silane. Barcoded transposed DNA and barcoded full-length cDNA from polyadenylated mRNA was amplified to fill gaps and generate sufficient amounts for library generation. The pre-amplified product was used for generation of both GEX and ATAC libraries. Single-cell gene expression libraries were generated using fragmentation, end repair, A-tailing and double-sided size selection using SPRIselect. P5 and P7 adaptor sequences were ligated and was further amplified with the number of PCR cycles depending on the number of nuclei loaded. Individual sample indices provided as a Dual Index Plate TT Set A (10x Genomics, 3000431) were used during amplification to enable pooling and subsequent demultiplexing of multiple libraries.    For ATAC libraries construction, P7 adapter sequences and sample indices from a Sample Index Plate N, Set A (10x Genomics, 3000427) were added to the pre-amplified product. Quantification and quality control of libraries was performed using High Sensitivity DNA assays on an Agilent Bioanalyzer. GEX expression libraries were sequenced on Illumina Novaseq. ATAC libraries were sequenced on Illumina Nextseq using custom sequencing read lengths 50-(8)i-(16)i-49.

tag: library type

value: multiome (gDNA+mRNA)


title: 48h_Multiome

status: Public on Apr 29 2023

type: SRA

city: Basel

first: Nadim

last: Aizarani

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

library_source: other

organism: Mus musculus

source_name: Gastruloids

growth_protocol: ESCs were grown in GMEM supplemented with 10% embryonic stem cell qualified FBS, GlutaMAX, sodium pyruvate, EmbryoMAX MEM NEAA, beta-mercaptoethanol, 0.1 µg/ml LIF, 3 µM CHIR99021, and 1 µM PD0305901. Gastruloids were generated from 300 cells and grown in 96-well ulta-low-attachment U-bottom plates in N2B27 medium (DMEM/F-12, Neurobasal medium, N2, B-27, GlutaMAX, HEPES, and beta-mercaptoethanol) and pulsed with 3 µM CHIR99021 from 48 to 72 hours.

treatment_protocol: Gastruloids were not treated.

tag: tissue

value: Gastruloids

tag: cell type

value: embryonic stem cells

tag: cell line

value: SBR (Sox1/Brachyury reporter)/CGR8

tag: strain


title: S3_52h

library_source: transcriptomic single cell

data_processing:
Reference and Quantification: Genome sequence and transcript annotation was obtained from Gencode Mouse release M24 (GRCm38 primary assembly and annotation gtf file from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M24), and the coordinates of transcripts and introns were extracted using R (https://r-project.org, version 3.6) and the getFeatureRanges function from the eisaR package (version 0.9 available from https://github.com/fmicompbio/eisaR/tree/bbd8787d7e4b87d158a276af0787226530867b88) with arguments featureType = c("spliced", "intron"), intronType = "separate", flankLength = 0, joinOverlappingIntrons = FALSE. A transcript-to-gene map was created using the getTx2Gene function from eisaR, which links transcripts to genes, and introns to distinct genes for simultaneous quantification (see below). Sequences were extracted from the genome using extractTranscriptSeqs from the GenomicFeatures package (version 1.38.2, )94 and indexed with Salmon (version 1.1.095) with arguments -k 23 –gencode and using the genome as a decoy. Reads were then quantified using Salmon/Alevin (version 1.1.096) with parameters -l ISR --chromiumV3 and the transcript-to-gene map created above.
Quality control and filtering: Technical quality of single cell experiments, cell barcode identification and quantification were assessed using the Bioconductor package alevinQC (version 1.4.0, https://doi.org/doi:10.18129/B9.bioc.alevinQC). Salmon/Alevin counts from all twelve timepoints were imported into R (version 4.0.2) using the tximeta package (version 1.6.397) and stored in a SingleCellExperiment container for downstream analysis. The number of detected genes per cell and the fraction of counts in genes encoded on the mitochondrion (chrM) were calculated using the addPerCellQC function from the scater package (version 1.16.298), and cells with more than 1800 detected genes and less than 10% mitochondrial counts were retained. Gms, mitochondrial, and ribosomal protein genes (genes associated with the GeneOntology term "structural constituent of ribosome", GO:0003735, based on the org.Mm.eg.db package, version 3.11.4) were removed, resulting in a final analysis set of 27027 genes and 71005 cells.
Assembly: GRCm38 primary assembly

molecule: total RNA

extract_protocol:
0h ESC, gastruloids 12, 24, 36, 48, 52, 56, 60, 72, 84,96, and 120 hours were dissociated with Accutase and per sample 12,000 alive cells were sorted by FACS. Cellular supensions were loaded on a 10x Genomics Chromium Single Cell instrument.
Single cell RNAseq libraries were prepared using the 10x Genomics Single Cell 3’ Gel Bead and Library Kit according to CG000183 Single Cell 3' Reagent Kit v3 User Guide_RevA. GEMRT was performed in a Bio-Rad PTC-200 Thermal Cycler with 0.2ml PCR Tube Strips (Eppendorf P/N 0030 124.359): 53 °C for 45 minutes, 85 °C for 5 minutes; held at 4 °C. After RT, GEMs were broken and the single strand cDNA was cleaned up with DynaBeads® MyOneTM Silane Beads (Life Technologies P/N 37002D). cDNA was amplified using a Bio-Rad PTC-200 Thermal cycler with 0.2ml PCR Tube Strips (Eppendorf P/N 0030 124.359): 98 °C for 3 min; cycled 11x: 98 °C for 15 s, 63 °C for 20 s, and 72 °C for 1 min; 72 °C for 1 min; held at 4 °C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit (0.6X SPRI). Indexed sequencing libraries were constructed using the reagents in the Chromium Single Cell 3’ library kit V3 ( 10x Genomics P/N1000078), following these steps: 1) Fragmentation, End Repair and A-Tailing; 2) Post Fragmentation, End Repair & A-Tailing Double Sided Size Selection with SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI); 3) adaptor ligation; 4) post-ligation cleanups with SPRIselect (0.8X SPRI); 5) sample index PCR using the Chromium Multiplex kit (10x Genomics P/N-120262); 6) Post Sample Index Double Sided Size Selection- with SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI). The barcode sequencing libraries were quantified using a Qubit 2.0 with a Qubit TM dsDNA HS Assay Kit (Invitrogen P/N Q32854) and the quality of the libraries were performed on a 2100 Bioanalyzer from Agilent using an Agilent High Sensitivity DNA kit (Agilent P/N 5067-4626). Sequencing libraries were loaded at 1.6pM on an Illumina Nextseq500 with 75cycle kits using the following read length: 28 cycles Read1, 8 cycles i7 Index and 56 cycles Read2.


title: S7.1_108h


title: S1_0h


title: ChIPseq_ESC_wt_p53_Act_r2

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

library_source: genomic

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10/hg19 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters, allowing only for uniquely mapping reads.
Assembly: mm10/hg19
Supplementary files format and content: wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and setting shift to 80. The scores in the wig file therefore represent the number of shifted alignments per 100bp window and per million reads in the library.

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). The human primary cell line (HMEC) were cultured in Mammary Epithelial Cell Growth Medium (Gibco MEGM) supplemented with growth factors (Gibco MEGM-SingleQuots CC-4136) BPE, hydrocortisone, hEGF, insulin and gentamicin/amphotericin-B (37°C, 7% CO2).

extract_protocol:
DNA was purified by Phenol:Chloroform extraction.
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 12 PCR cycles.

treatment_protocol: Cells (1.5x10^7) were seeded into 15 cm plates the day before the experiment. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) chromatin was sonicated for 22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (2) 75ug of chromatin was used per IP, (3) protein A magnetic Dynabeads (Thermo Fisher Scientific) were used.

tag: genotype

value: wild type

tag: treatment condition

value: activated p53

tag: chip antibody

value: Cell Signaling technologies, p53(1C12) mAb#2524


title: S2_48h


title: S4_56h


title: ATACseq_ESC_dTrim24_IRDegrAct_r2

data_processing:
Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. ATAC-seq reads were trimmed using cutadapt version 1.18, (Martin, M. EMBnet.journal 17, 10 (2011)) with parameters -a CTGTCTCTTATACACA -A CTGTCTCTTATACACA -m 5 --overlap=1 and then mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters.
Supplementary files format and content: wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 and pairedAsSingle=TRUE . The scores in the wig file therefore represent the number of 5'-read ends (Tn5 insertion sites) per 100bp window and per million reads in the library.

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol: DNA was purified using the MinElute PCR Purification Kit (Qiagen).

treatment_protocol: Cells (0.25x10^6) were seeded into 6-well plates the day before the experiment. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles. For activation of p53 via alternative pathways, cells were treated with 20 µM nutlin3a or cells were subjected to 60Gy ionizing radiation and left for 4 hours. ATAC-seq was performed according to the previously described protocol(Corces, M. R. et al. Nat. Methods, 2017) with modifications. Briefly, 5x10^4 cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500g for 5 min in a pre-chilled (4°C). Cell pellets were suspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g (4°C). Nuclei were suspended in 50 μl of Tn5 transposition mix (25 μl 2× TD buffer, 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermomixer with shaking at 1,000 rpm. Reactions were cleaned up using the MinElute PCR Purification Kit (Qiagen). The eluted transposed DNA was subjected to PCR amplification using Q5 High-Fidelity Polymerase (NEB) for 7 cycles.

value: degron-tagged Trim24

value: degraded Trim24; IR activated p53


title: ATACseq_ESC_dTrim24_IRAct_r1

value: IR activated p53


title: ATACseq_ESC_dTrim24_NutlinDegrAct_r1

value: degraded Trim24; Nutlin activated p53


title: ATACseq_ESC_dTrim24_IRDegrAct_r1


title: ATACseq_ESC_dTrim24_IRAct_r2


title: ATACseq_ESC_dTrim24_NutlinAct_r2

value: Nutlin activated p53


title: ATACseq_ESC_dTrim24_NutlinAct_r1


title: ATACseq_ESC_dTrim24_DegrAct_8h_r1

value: degraded Trim24; activated p53 - 8 hour


title: ATACseq_ESC_dTrim24_DegrAct_4h_r2

value: degraded Trim24; activated p53 - 4 hour


title: ATACseq_ESC_dTrim24_DegrAct_4h_r1


title: S6_96h


title: ATACseq_ESC_dTrim24_DegrAct_2h_r2

value: degraded Trim24; activated p53 - 2 hour


title: ATACseq_ESC_dTrim24_DegrAct_2h_r1


title: ATACseq_ESC_dTrim24_DegrAct_1h_r2

value: degraded Trim24; activated p53 - 1 hour


title: ATACseq_ESC_dTrim24_DegrAct_0h_r1

value: degraded Trim24; activated p53 - 0 hour


title: ATACseq_ESC_dTrim24_Act_12h_r1

value: activated p53 - 12 hour


title: ATACseq_ESC_dTrim24_DegrAct_1h_r1


title: ATACseq_ESC_dTrim24_Act_8h_r1

value: activated p53 - 8 hour


title: ATACseq_ESC_dTrim24_Act_4h_r2

value: embryonic stem cells

value: activated p53 - 4 hour


title: ATACseq_ESC_dTrim24_NutlinDegrAct_r2


title: ATACseq_ESC_dTrim24_DegrAct_12h_r1

value: degraded Trim24; activated p53 - 12 hour


title: ATACseq_ESC_dTrim24_Act_8h_r2


title: ATACseq_ESC_dTrim24_Act_2h_r2

value: activated p53 - 2 hour


title: ATACseq_ESC_dTrim24_DegrAct_8h_r2


title: ATACseq_ESC_dTrim24_Act_1h_r2

value: activated p53 - 1 hour


title: ATACseq_ESC_dTrim24_Act_4h_r1

value: degron-tagged Trim24


title: ATACseq_ESC_dTrim24_Act_1h_r1


title: ATACseq_ESC_dTrim24_Act_0h_r1

value: activated p53 - 0 hour


title: ATACseq_ESC_dTrim24_DegrAct_r1

value: degraded Trim24; activated p53


title: ATACseq_ESC_dTrim24_DegrAct_r3


title: ATACseq_Neuron_dTrim24_DegrAct_r2

source_name: differentiated neuronal cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). For neural differentiation, dishes were coated with sterile filtered (0.22μm) Poly-D-lysine hydrobromide (0.5mg/ml, Sigma, P-7886-100MG) diluted in Borate Buffer (50mM, pH 8.5) for 24 hours at 37oC, washed 3x with sterile water and coated for at least 2 hours with Laminin (6.65ug/ml, Sigma, L2020-1MG) in PBS at 37oC. To differentiate mouse ES cells they were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008), trypsinated and plated at a density of 0.2x10^6 per well in proliferation medium (DMEM/F12 with Glutamax (LifeTech 31331-028), 1× B27 supplement without vitamin A (LifeTech 12587-010), 1× N2 supplement (LifeTech 17502-048)) supplemented with 1μg/ml Doxycycline for three days to generate neurons.

treatment_protocol: mES Cells (0.25x10^6) were seeded into 6-well plates the day before the experiment. Neurons were generated by seeding cells into 6-well plates three days befor the experiment and treating with differentiation conditions. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles. For activation of p53 via alternative pathways, cells were treated with 20 µM nutlin3a or cells were subjected to 60Gy ionizing radiation and left for 4 hours. ATAC-seq was performed according to the previously described protocol(Corces, M. R. et al. Nat. Methods, 2017) with modifications. Briefly, 5x10^4 cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500g for 5 min in a pre-chilled (4°C). Cell pellets were suspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 g (4°C). Nuclei were suspended in 50 μl of Tn5 transposition mix (25 μl 2× TD buffer, 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermomixer with shaking at 1,000 rpm. Reactions were cleaned up using the MinElute PCR Purification Kit (Qiagen). The eluted transposed DNA was subjected to PCR amplification using Q5 High-Fidelity Polymerase (NEB) for 7 cycles.

value: differentiated neuronal cells

value: degron-tagged Trim24; Ngn2Piggyback vector


title: ATACseq_ESC_dTrim24_Act_r2

value: activated p53


title: ATACseq_ESC_dTrim24_Unt_r2

value: basal p53


title: ATACseq_ESC_dTrim24_Unt_r3


title: ATACseq_ESC_dTrim24_Act_r1


title: ATACseq_ESC_dTrim24_Act_r3


title: ATACseq_ESC_dTrim24_Unt_r1


title: ATACseq_ESC_dTrim24_Act_2h_r1


title: ATACseq_Neuron_dTrim24_Act_r2


title: ATACseq_Neuron_dTrim24_DegrAct_r1


title: ATACseq_ESC_dTrim24_Degr_r3

value: degraded Trim24


title: scRNAseq of lung metastasis derived from PyMT/GPx2 KD mammary tumor model

city: Bronx

first: Rachel

last: Hazan

state: NY

address: 1300 Morris Park Avenue

department: Pathology

country: USA

institute: Albert Einstein College of Medicine

data_processing: The original data obtained from Illumina   HiSeq platform (Novogene Corp, Sacramento, CA), were transformed to sequenced reads by base calling. Raw data obtained as FASTQ files which contain sequenced reads were subjected to quality control using OpenGene   s fastp v0.19.4 preprocessor64. Cellranger 3.0.2. software was used to provide reads alignment and gene annotation to the mm10 mouse reference genome. The STAR aligner employed within cellranger 3.0.2 was used to perform alignment. Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were quantified using each cell-barcode in combination with unique molecular identifiers (UMIs) using the default cellranger. The quantified UMI counts were used to form an unfiltered gene-barcode matrix and exported for further downstream analysis.

source_name: Mammary tumor

extract_protocol:
PyMT1 control, PyMT1/GPx2 KD tumor, and lung metastases (from paired PyMT1/GPx2 KD primary tumor) generated by injection of GFP-labelled tumor cell lines, was excised and mechanically chopped with scalpels, incubated in DMEM/F12 with 5% FBS, 5   g/ml insulin, 2 mg/ml collagenase, and 150   g/mL DNase at 37   C for 45 min. Cell clamps were washed and dissociated with 2 ml of 0.05% trypsin/EDTA at 37 0C for 10 min and trypsinization stopped with 10ml PBS-2%FBS-EDTA. The samples were filtered through a 70   m cell strainer, pelleted at 1200 rpm at 4 0C for 5 min, and resuspended  in 1 ml of 1x red blood cell (RBC) lysis buffer and 10ml PBS-2%FBS-EDTA was added to stop lysis. Cells pellets were resuspended in 1ml PBS-2%FBS-EDTA and viability-controlled by trypan blue dye exclusion.
Library preparation was performed by Mr. David Reynolds at the AECOM genomic core facility. GFP-sorted single cell suspensions from PyMT1 control, PyMT1/GPx2 KD tumor, and lung metastases containing at least 80% viable cells were processed to capture at least ~10,000 viable cells per sample. The libraries were prepared (individual lanes on the 10X Chromium) using the 10X Single Cell 3    v3 kit using ~10,000 cells per lane on the 10X Chromium microfluidics device (10X Genomics, Pleasanton, CA). The qualified libraries were sequenced on Illumina Hiseq 6000 platform (Novogene Corp, Sacramento, CA), with a standard paired-end 150bp (PE150) at each end.

value: Mammary tumor

tag: metastasis site

value: lung


title: ATACseq_ESC_dTrim24_Degr_r1


title: ATACseq_Neuron_dTrim24_Act_r1


title: ATACseq_ESC_dp53_Act_r2

value: degron-tagged p53


title: ATACseq_ESC_dp53_Act_r1


title: ATACseq_Neuron_dTrim24_Unt_r1


title: ATACseq_ESC_dTrim24_Degr_r2


title: ATACseq_Neuron_dTrim24_Degr_r1


title: ATACseq_ESC_dTrim24_DegrAct_r2


title: ATACseq_Neuron_dTrim24_Unt_r2


title: ATACseq_ESC_dp53_Degr_r2

value: degraded p53


title: ATACseq_ESC_dp53_Unt_r1

value: embryonic stem cells


title: ATACseq_ESC_dp53_Unt_r2


title: ChIPseq_Neuron_dTrim24_IgG_Act_r2

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). The human primary cell line (HMEC) were cultured in Mammary Epithelial Cell Growth Medium (Gibco MEGM) supplemented with growth factors (Gibco MEGM-SingleQuots CC-4136) BPE, hydrocortisone, hEGF, insulin and gentamicin/amphotericin-B (37°C, 7% CO2). For neural differentiation, dishes were coated with sterile filtered (0.22μm) Poly-D-lysine hydrobromide (0.5mg/ml, Sigma, P-7886-100MG) diluted in Borate Buffer (50mM, pH 8.5) for 24 hours at 37oC, washed 3x with sterile water and coated for at least 2 hours with Laminin (6.65ug/ml, Sigma, L2020-1MG) in PBS at 37oC. To differentiate mouse ES cells they were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008), trypsinated and plated at a density of 7.5x10^6 per 15cm dish in proliferation medium (DMEM/F12 with Glutamax (LifeTech 31331-028), 1× B27 supplement without vitamin A (LifeTech 12587-010), 1× N2 supplement (LifeTech 17502-048)) supplemented with 1μg/ml Doxycycline for three days to generate neurons.

treatment_protocol: Cells (1.5x10^7) were seeded into 15 cm plates the day before the experiment. Neurons were generated by seeding cells into 6-well plates three days befor the experiment and treating with differentiation conditions. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) chromatin was sonicated for 22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (2) 75ug of chromatin was used per IP, (3) protein A magnetic Dynabeads (Thermo Fisher Scientific) were used.

value: Sigma Aldrich, IgG M7023


title: ChIPseq_HMEC_wt_IgG_Unt_r1

organism: Homo sapiens

source_name: Mammary Epithelial Cells

value: Mammary Epithelial Cells

value: wild type

value: Normal Human Mammary Epithelial Cells CC-2551


title: ATACseq_Neuron_dTrim24_Degr_r2


title: ChIPseq_HMEC_wt_p53_Act_r1

value: Cell Signaling technologies, p53(1C12) mAb#2524


title: ATACseq_ESC_wt_Act_r2


title: ChIPseq_HMEC_wt_p53_Unt_r1


title: ATACseq_ESC_wt_Act_r1


title: ATACseq_ESC_wt_Unt_r2


title: ChIPseq_Neuron_dTrim24_Trim24_Act_r1

value: Bethyl Laboratories, Trim24 A300-815A


title: ChIPseq_Neuron_dTrim24_IgG_Act_r1


title: ChIPseq_ESC_dp53_H3K27ac_Act_r1

value: Active Motif, H3K27ac 39133


title: ChIPseq_ESC_dp53_H3K27ac_Act_r2


title: ATACseq_ESC_wt_Unt_r1


title: ChIPseq_ESC_dp53_H3K27ac_Unt_r1


title: ChIPseq_Neuron_dTrim24_p53_Act_r1

value: differentiated neuronal cells


title: ChIPseq_ESC_dp53_H3K27ac_Degr_r2


title: ChIPseq_ESC_dp53_H3K27ac_Unt_r2


title: ChIPseq_ESC_dp53_IgG_Unt_r1


title: ChIPseq_ESC_dp53_p53_Act_r2


title: ChIPseq_ESC_dp53_p53_Unt_r2


title: ATACseq_ESC_dp53_Degr_r1


title: ChIPseq_ESC_dp53_H3K27ac_Degr_r1


title: ChIPseq_Neuron_dTrim24_p53_Act_r2

value: degron-tagged Trim24; Ngn2Piggyback vector


title: Immune_K3shIL33KD_3

status: Public on Apr 27 2023

city: New York City

first: Cassandra

last: Burdziak

state: New York

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: 10x Genomics (3' kit, v2.0)

data_processing:
The demultiplexing, barcoded processing, alignment, and count matrix generation was done using the SEQC software.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary files format and content: ProgressionCohort.h5ad: AnnData file containing processed scRNA-seq counts for the entire epithelial Progression Cohort. Counts are normalized but un-logged, and raw data is available in the .raw attribute.
Supplementary files format and content: Combined_ImmuneEpi.h5ad: AnnData file containing processed scRNA-seq counts for the entire epithelial and immune Progression Cohort. Counts are normalized but un-logged.
Supplementary files format and content: PerturbationCohort_K3.h5ad: AnnData file containing processed scRNA-seq counts for epithelial cells from K3 condition with and without IL-33 perturbation. Counts are log-normalized.

source_name: pancreas

growth_protocol: When indicated, 5 weeks-old KC;RIK (p48-Cre;RIK;LSLKrasG12D) littermate male mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) for 2 consecutive days.

extract_protocol:
Single-cell encapsulation and scRNA-seq library prep of FACS-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v2). Each sample loaded onto the cartridge contained approximately 5,000 cells at a final dilution of ~500 cells/μl. Transcriptomes of encapsulated cells were barcoded during reverse transcription.
cDNA was purified with DynaBeads, followed by amplification per the user manual (Reagent Kit 3’ v2). Next, the PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads.

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC or CD45-APC-Cy7 antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, CD45-negative and DAPI-negative) or immune cells (marked as mKate2-negative, CD45-positive and DAPI-negative) were sorted using Aria3 or Aria 1 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS).  Single-cell suspensions were spun down and resuspended in 0.05% BSA containing 1 U/µL Invitrogen Ambion RNase Inhibitor (AM2682, Thermo Fisher Scientific).

value: sorted primary CD45+ immune cells

value: pancreas

tag: condition

tag: model

value: KC;RIK-shIl33.668 (On Dox)

tag: alleles

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Il33 (sh668)

tag: treatment

value: Caerulein / Week 3

tag: sorting strategy

tag: time point_(analyses)

value: 8-9 weeks old

tag: Sex

value: Male


title: Immune_K3shIL33KD_2

description: 10x Genomics (3' kit, v2.0)


title: ChIPseq_Neuron_dTrim24_Trim24_Act_r2

value: activated p53


title: ChIPseq_ESC_dp53_p53_Act_r1

value: embryonic stem cells

value: degron-tagged p53


title: tlr2-/-, 5 dpf, 3

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: 150 nucleotides

library_source: transcriptomic

data_processing:
RNAseq reads of tlr2 mutant and wild type control were aligned and mapped to the zebrafish ge-nome GRCz11 using Salmon v1.2.1
Differential gene expression was analyzed by using DESeq2 v1.24.0. Statistical significance was determined by an S value of ≤ 0.005 by utilizing apeglm.
Assembly: the zebrafish genome GRCz11
Supplementary files format and content: excel files include normalized read values per million for each sample and ratios and s values of tlr2 mutant and wild type control zebrafish larvae

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://zfin.org).

extract_protocol:
Zebrafish larvae from  all groups  groups (n=3) were resuspended and crushed in 0.5 ml of TRIzol Reagent
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was used to process the samples. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation of the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

value: tlr2 mutant

value: whole embryos

tag: age

value: 5 days post fertilization


title: tlr2-/-, 5 dpf, 1

description: 150 nucleotides


title: ChIPseq_ESC_dp53_IgG_Unt_r2

value: basal p53

value: Sigma Aldrich, IgG M7023


title: tlr2-/-, 5 dpf, 2

description: 150 nucleotides


title: Immune_K2shIL33KD_1

description: 10x Genomics (3' kit, v2.0)

value: Caerulein / Day 2

value: 5-6 weeks old


title: Immune_K3shControl_2

description: 10x Genomics (3' kit, v2.0)

value: sorted primary CD45+ immune cells

value: KC;RIK-shIl33.668 (Off Dox)


title: Immune_K3shControl_1

description: 10x Genomics (3' kit, v2.0)

value: pancreas


title: Immune_K2shIL33KD_2

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shIl33.668 (On Dox)

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Il33 (sh668)


title: Immune_K1_3

description: 10x Genomics (3' kit, v2.0)

value: PBS / Day 2


title: Immune_K1_2

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK

value: Male


title: tlr2+/+, 5 dpf, 2

description: 150 nucleotides

value: wild type


title: Immune_K3_1

description: 10x Genomics (3' kit, v2.0)

value: Caerulein / Week 3

value: 8-9 weeks old


title: Immune_K3shIL33KD_1

description: 10x Genomics (3' kit, v2.0)


title: tlr2+/+, 5 dpf, 3

description: 150 nucleotides

value: whole embryos


title: Immune_K1_1

description: 10x Genomics (3' kit, v2.0)


title: Immune_K2-Day1_1

description: 10x Genomics (3' kit, v2.0)

value: Caerulein / Day 1

value: 5 weeks old


title: ChIPseq_ESC_dp53_p53_Unt_r1

value: embryonic stem cells

value: degron-tagged p53

value: basal p53

value: Cell Signaling technologies, p53(1C12) mAb#2524


title: Immune_K2_1

description: 10x Genomics (3' kit, v2.0)

value: sorted primary CD45+ immune cells

value: Caerulein / Day 2

value: 5-6 weeks old


title: Immune_K3_2

description: 10x Genomics (3' kit, v2.0)

value: pancreas


title: Immune_K3shIL33KD_4

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shIl33.327 (On Dox)

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Il33 (sh327)


title: Epithelial_K3shControl_2

description: 10x Genomics (3' kit, v2.0)

value: sorted primary pancreatic epithelial cells (mKate2+)

value: KC;RIK-shIl33.327 (Off Dox)

value: Male


title: Epithelial_K3shIL33KD_1

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shIl33.668 (On Dox)

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Il33 (sh668)

value: Caerulein / Week 3

value: 8-9 weeks old


title: tlr2+/+, 5 dpf, 1

description: 150 nucleotides

value: wild type

value: whole embryos

value: 5 days post fertilization


title: Immune_K2shControl_2

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shRen.713 (On Dox)

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Renilla (sh713)


title: Epithelial_K3shIL33KD_3

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shIl33.327 (OnDox)


title: Epithelial_N2_1

description: 10x Genomics (3' kit, v2.0)

value: C;RIK

value: Caerulein / Day 2

value: 5-6 weeks old


title: Epithelial_K3shIL33KD_2

description: 10x Genomics (3' kit, v2.0)

value: pancreas


title: Epithelial_K2shIL33KD_2

description: 10x Genomics (3' kit, v2.0)

value: sorted primary pancreatic epithelial cells (mKate2+)


title: Epithelial_K2shControl_2

description: 10x Genomics (3' kit, v2.0)


title: Epithelial_K3shControl_1

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shIl33.668 (Off Dox)


title: Epithelial_K2shIL33KD_3

description: 10x Genomics (3' kit, v2.0)

value: Male


title: Epithelial_K2shIL33KD_1

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shIl33.668 (On Dox)


title: Epithelial_K6_4.2

description: 10x Genomics (3' kit, v2.0)

value: KPC;RIK

value: PDAC lesion (Lung Metastases)

value: PDAC lesion


title: Epithelial_K2shControl_1

description: 10x Genomics (3' kit, v2.0)

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Il33 (sh668)


title: Epithelial_K5_3

description: 10x Genomics (3' kit, v2.0)

value: PDAC lesion (Primary Tumor)


title: Epithelial_K6_1

description: 10x Genomics (3' kit, v2.0)


title: Epithelial_K4_1

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK

value: 27 weeks old


title: Epithelial_K5_4

description: 10x Genomics (3' kit, v2.0)


title: Epithelial_K4_2

description: 10x Genomics (3' kit, v2.0)


title: Epithelial_K5_1

description: 10x Genomics (3' kit, v2.0)


title: Epithelial_K3_1

description: 10x Genomics (3' kit, v2.0)

value: Caerulein / Week 3

value: 8-9 weeks old


title: Epithelial_K1_3

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shRNA (Off Dox)

value: PBS / Day 2


title: Epithelial_K1_2

description: 10x Genomics (3' kit, v2.0)

value: 5-6 weeks old


title: Epithelial_K1.5_2

description: 10x Genomics (3' kit, v2.0)

value: pancreas

value: PBS / Week 3


title: Epithelial_K1.5_1

description: 10x Genomics (3' kit, v2.0)

value: sorted primary pancreatic epithelial cells (mKate2+)


title: Epithelial_K1_1

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK-shRen.713 (Off Dox)

value: Male


title: Epithelial_N1_2

description: 10x Genomics (3' kit, v2.0)

value: C;RIK


title: Epithelial_N1_1

description: 10x Genomics (3' kit, v2.0)


title: Epithelial_K2-Day1_1

description: 10x Genomics (3' kit, v2.0)

value: Caerulein / Day 1


title: Epithelial_K3_2

description: 10x Genomics (3' kit, v2.0)


title: Epithelial_K2_1

description: 10x Genomics (3' kit, v2.0)

value: Caerulein / Day 2


title: Epithelial_K5_scATAC1

description: 10x Genomics

library_source: genomic single cell

data_processing:
De-multiplexing, barcode processing, alignment, and counting matrix generation was performed with modified CellRanger ATAC.
Assembly: mm10
Supplementary files format and content: H5 files with peak by cell matrices.
Supplementary files format and content: ProgressionCohort_scATAC.h5ad: AnnData file containing processed scATAC-seq ArchR gene scores for all epithelial cells collected for scATAC.

extract_protocol:
FACS-sorted cells were lysed in cold-lysis buffer (0.1% NP-40, 0.1% Tween 20, 0.01% Digitonin, 10 mM NaCl, 3 mM MgCl2 and 10 mM Tris-HCl [pH 7.4]), washed and processed according to “Nuclei Isolation for Single-Cell ATAC Sequencing” protocol (CG000169 RevD). Resulting nuclei suspension was subjected to transposition reaction for 60 min at 37°C and then encapsulated in microfluidic droplets using 10X Chromium instrument following manufacturer’s instructions with a targeted nuclei recovery ~ 5,000.
Barcoded DNA material was cleaned and prepared for sequencing according to the Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics; CG000168 RevA). Purified libraries were assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent) and sequenced on a Illumina HiSeq 2500 (High Output) platform at approx. 150M reads (R1 50bp, R2 50 bp, i7 8bp, i5 16bp) per 1 sample (~ 5000 nuclei) at MSKCC’s Integrated Genomics Operation Core.

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC or CD45-APC-Cy7 antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS).

value: KPflC;RIK

value: Full-blown PDAC lesion


title: Epithelial_N2_2

description: 10x Genomics (3' kit, v2.0)


title: Epithelial_K5_scATAC2

description: 10x Genomics


title: Epithelial_K3_scATAC1

description: 10x Genomics

value: KC;RIK

value: Caerulein / 3 weeks

value: 8 weeks old (3 weeks post-Caerulein)


title: Epithelial_K3_scATAC2

description: 10x Genomics


title: Epithelial_K6_4.1

description: 10x Genomics (3' kit, v2.0)

value: KPC;RIK

value: PDAC lesion (Liver Metastases)

value: PDAC lesion


title: Day 14 Replicate 4

status: Public on Apr 26 2023

city: Ithaca

first: Vimal

last: Selvaraj

address: 204 Morrison Hall

department: Animal Sciences

institute: Cornell University

data_processing:
The quality of raw reads was checked using FastQC before aligning to bovine reference genome (ARS UCD 1.2) using R package STAR
Differentially expressed genes were identified using R package EdgeR

organism: Bos taurus

source_name: Day 14 bovine endometrium

extract_protocol:
Total RNA was isolated using RNAqueous Micro Total RNA isolation kit.
mRNA was captured using poly (A) and cDNA libraries were prepared using TruSeq stranded total RNA sample preparation kit (Illumina)

treatment_protocol: Cattle (Holstein virgin heifers) at least 7 months of age, sexually mature, non-lactating and weighing at least 340 kg (750 lbs) were subjected to estrous cycle synchronization, five-day Co-synch. In brief, a GnRH analog (100 μg intra-muscular, Fertagyl, MWI Animal Health) and progesterone (1.38g in a controlled intra-vaginal drug release device, Eazi-Breed, Zoetis) were administered. After 96 hours, a prostaglandin F2α analog Estrumate (500 μg intra-muscular, Cloprostenol, MWI Animal Health) was administered, followed by a second dose of Estrumate (500 μg intra-muscular, Cloprostenol, MWI Animal Health) and removal of the Eazi-Breed device at 120 hours. Fourty-eight hours after removal of the Eazi-Breed device, timed artifiical insemination (TAI) was performed using Holstein semen. The synchronized animals were randomly selected for one of five early pregnancy  timepoints [day 0 (estrus), 5,10,14 and 18; n=4/timepoint] for endometrial biopsies.

value: Bovine endometrium


title: Day 18 Replicate 1

source_name: Day 18 bovine endometrium


title: Day 18 Replicate 2


title: Day 18 Replicate 4


title: Day 18 Replicate 3


title: Day 14 Replicate 3


title: Day 14 Replicate 1


title: Day 14 Replicate 2


title: Day 10 Replicate 2

source_name: Day 10 bovine endometrium


title: Day 10 Replicate 1


title: Day 10 Replicate 4


title: Day 5 Replicate 4

source_name: Day 5 bovine endometrium


title: Day 5 Replicate 3


title: Sample26_DRUG_4_Exp_60716_S81

status: Public on Apr 22 2023

city: New York

first: Dr. Chiara

last: Giannarelli

address: 435 E 30th St

department: Cardiology

institute: NYU Langone Health

description: RNA bulk sequencing

data_processing:
Quality control of RNA-seq data was performed using FastQC2 v.0.11.7, a final report was generated for each FASTQ file to
assess general sequencing quality. Raw sequenced reads were trimmed using fastp3 v0.20.1 for
quality of bases and to eliminate sequencing adaptors. Following that the raw reads were aligned
using STAR v.2.6.1d with hg38 as the reference genome. The gene-level expression counts were
computed with featureCounts function in the Subread package (v.1.6.3; parameters: -g gene_id )
using the human gene annotations from Gencode release 33.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include rawcounts for each Sample

source_name: peripheral blood mononuclear cells

growth_protocol: Pbmcs of healthy donors were isolated and resuspended in RPMI-1640 medium containing 10% fetal bovine serum, 1x penicillin/streptomycin, and benzonase (25 U/ml), washed and resuspended in warm media.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
Automated stranded RNA-seq library poly-A preparation.

treatment_protocol:
Pbmcs from healthy donors were diluted at 2x10^6 cells/ml in RPMI-1640 medium containing 1% FBS and 1x P/S, and then plated into a 96-well deep well plate and put at rest for 2 hours.
Next, PBMCs were pre-incubated with each drug for 30 minutes at the following concentrations:  Drug 1: Ro 31_8220 mesylate (10 µM; Selleckchem, Cat# S7207); Drug 2: Alvocidib (1 µM; Selleckchem, Cat# S1230); Drug 3: AZD8055 (10 µM, Selleckchem, Cat# S1555); Drug 4: Saracatinib (10 µM; Selleckchem, Cat# S1006); Drug 5: PF_562271 HCl (10 µM; Selleckchem, Cat# S7357);
PMBCs were then stimulated with plasma taken from atherosclerotic patients at a final concentration of 20% -/+ drugs or vehicle (DMSO) and incubated at 37°C in 5% CO2 incubator. Cells were harvested after 3 hrs incubation.

value: peripheral blood mononuclear cells

value: plasma stimulation -/+ drug 4


title: Sample26_DRUG_5_Exp_60716_S82

description: RNA bulk sequencing

value: plasma stimulation -/+ drug 5


title: Sample26_DRUG_3_Exp_60716_S80

description: RNA bulk sequencing

value: plasma stimulation -/+ drug 3


title: Sample25_VEHICLE_Exp_60716_S67

description: RNA bulk sequencing

value: plasma stimulation + vehicle


title: Day 5 Replicate 1


title: Sample26_VEHICLE_Exp_60716_S77

description: RNA bulk sequencing


title: Sample25_DRUG_4_Exp_60716_S71

description: RNA bulk sequencing


title: Sample26_DRUG_1_Exp_60716_S78

description: RNA bulk sequencing

value: plasma stimulation + drug 1


title: Sample26_DRUG_2_Exp_60716_S79

description: RNA bulk sequencing

value: plasma stimulation -/+ drug 2


title: Day 5 Replicate 2


title: Sample25_DRUG_3_Exp_60716_S70

description: RNA bulk sequencing


title: Sample25__DRUG_1_Exp_60716_S68

description: RNA bulk sequencing


title: Sample25__DRUG_2_Exp_60716_S69

description: RNA bulk sequencing


title: Sample25_DRUG_5_Exp_60716_S72

description: RNA bulk sequencing


title: Sample11-DRUG-5-2_S24

description: RNA bulk sequencing


title: Sample11-DRUG-4-2_S20

description: RNA bulk sequencing


title: Sample11-DRUG-3-2_S16

description: RNA bulk sequencing


title: Sample11-DRUG-5-1_S23

description: RNA bulk sequencing


title: Sample11-DRUG-4-1_S19

description: RNA bulk sequencing


title: Day 10 Replicate 3


title: Sample11-DRUG-3-1_S15

description: RNA bulk sequencing


title: Sample11-DRUG-2-2_S12

description: RNA bulk sequencing


title: Sample11-DRUG-1-2_S8

description: RNA bulk sequencing


title: Sample11-DRUG-2-1_S11

description: RNA bulk sequencing


title: Sample9-DRUG-5-2_S22

description: RNA bulk sequencing


title: Sample11-VEHICLE-1_S3

description: RNA bulk sequencing


title: Sample11-VEHICLE-2_S4

description: RNA bulk sequencing


title: Sample11-DRUG-1-1_S7

description: RNA bulk sequencing


title: Sample9-DRUG-4-1_S17

description: RNA bulk sequencing


title: Sample9-DRUG-4-2_S18

description: RNA bulk sequencing


title: Immune_K2shIL33KD_3

description: 10x Genomics (3' kit, v2.0)

value: sorted primary CD45+ immune cells

value: pancreas

value: KC;RIK-shIl33.668 (On Dox)

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Il33 (sh668)

value: Caerulein / Day 2

value: 5-6 weeks old

value: Male


title: Sample9-DRUG-2-1_S9

description: RNA bulk sequencing


title: Sample9-DRUG-3-1_S13

description: RNA bulk sequencing


title: Sample9-DRUG-1-2_S6

description: RNA bulk sequencing


title: Sample9-VEHICLE-2_S2

description: RNA bulk sequencing


title: Sample9-DRUG-3-2_S14

description: RNA bulk sequencing


title: Disease plasma_PBMC_8_S8_L002

description: RNA bulk sequencing

data_processing:
Quality control of RNA-seq data was performed using the pipeline RAPiD-nf. FastQCv.0.11.6, a final report was generated for each FASTQ file to
assess general sequencing quality.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include rawcounts for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
Automated stranded RNA-seq library poly-A preparation.

treatment_protocol:
Pbmcs diluted at 2x10^6 cells/ml in RPMI-1640 medium containing 1% FBS, 1x P/S, were then plated into a 96-well deep well plate and put to rest at 37°C in 5% CO2 incubator for 2hrs.
Cell were then stimulated using either plasma isolated from atherosclerotic patients (disease plasma) or control plasma from healthy donors (healthy plasma) at a final concentration of 20% and incubated for 3 hrs at 37°C and 5% CO2.

value: patient plasma stimulation


title: Disease plasma_PBMC_7_S7_L002

description: RNA bulk sequencing


title: Sample9-DRUG-2-2_S10

description: RNA bulk sequencing


title: Disease plasma_PBMC_9_S9_L002

description: RNA bulk sequencing


title: Sample9-VEHICLE-1_S1

description: RNA bulk sequencing


title: Disease plasma_PBMC_6_S6_L002

description: RNA bulk sequencing


title: Disease plasma_PBMC_4_S3_L002

description: RNA bulk sequencing


title: Disease plasma_PBMC_5_S2_L002

description: RNA bulk sequencing


title: Sample9-DRUG-1-1_S5

description: RNA bulk sequencing


title: Disease plasma_PBMC_3_S4_L002

description: RNA bulk sequencing


title: Disease plasma_PBMC_2_S5_L002

description: RNA bulk sequencing


title: Disease plasma_PBMC_1_S1_L002

description: RNA bulk sequencing


title: Healthy plasma_PBMC_15_S15_L002

description: RNA bulk sequencing

value: healthy donor plasma stimulation


title: Healthy plasma_PBMC_14_S14_L002

description: RNA bulk sequencing


title: Healthy plasma_PBMC_13_S13_L002

description: RNA bulk sequencing


title: Sample9-DRUG-5-1_S21

description: RNA bulk sequencing


title: Healthy plasma_PBMC_16_S16_L002

description: RNA bulk sequencing


title: Healthy plasma_PBMC_12_S12_L002

description: RNA bulk sequencing


title: Disease plasma_PBMC_10_S10_L002

description: RNA bulk sequencing


title: Disease plasma_PBMC_1_S1_L001

description: RNA bulk sequencing


title: Disease plasma_PBMC_4_S3_L001

description: RNA bulk sequencing


title: Disease plasma_PBMC_2_S5_L001

description: RNA bulk sequencing


title: Disease plasma_PBMC_3_S4_L001

description: RNA bulk sequencing


title: Disease plasma_PBMC_5_S2_L001

description: RNA bulk sequencing


title: Healthy plasma_PBMC_11_S11_L002

description: RNA bulk sequencing


title: Disease plasma_PBMC_6_S6_L001

description: RNA bulk sequencing


title: Disease plasma_PBMC_9_S9_L001

description: RNA bulk sequencing


title: Healthy plasma_PBMC_13_S13_L001

description: RNA bulk sequencing


title: Healthy plasma_PBMC_15_S15_L001

description: RNA bulk sequencing


title: Disease plasma_PBMC_8_S8_L001

description: RNA bulk sequencing


title: Healthy plasma_PBMC_16_S16_L001

description: RNA bulk sequencing


title: S2 cell, WT, Input, rep1 [re-used]

status: Public on Apr 19 2023

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
Reads were trimmed using Trim Galore v0.6.5 and then aligned to the reference genome (dm3) using Bowtie v2.3.5 with default parameters. The PCR duplicates for each dataset were removed using the rmdup function of samtools v1.13. The data reproducibility between biological replicates was confirmed, then reads from replicates were pooled together for further analysis. Peak calling was performed with MACS v2.2.5 with parameters: -g dm -q 0.05 --nomodel --extsize 300. H3K27me3 and H3K27ac were called as broad peaks, while all other factors were called as narrow peaks. Differential binding analysis was performed using DiffBind2, with summit set as 250. Overlap of peaks were performed using the window function from BEDTools v2.29.2. ChIP-seq tracks were visualized using IGV, and heatmaps were created using DeepTools v3.5.1.
Assembly: dm3
Supplementary files format and content: narrowPeak (except for Input sample)

organism: Drosophila melanogaster

source_name: 3rd instar larval imaginal discs and brains

extract_protocol:
Chromatin immunoprecipitation (X-ChIP) was prepared as describe previously (Erokhin et al., BMC Biol, 2021). For each experiment, 150-200 mg of 3rd instar larvae or embryos were collected. The material was homogenized in 5 ml of buffer A1 (15 mM HEPES, pH 7.6; 60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 0.5% Triton X-100, 0.5 mM DTT, Roche cOmplete protease inhibitor) supplemented with the EDTA-free protease inhibitor cocktail (Roche, Switzerland) and formaldehyde as a crosslinking agent (final concentration 1.8%). The reaction was stopped by adding glycine (final concentration 225 mM). The homogenate was cleared by passing through 100-µm nylon cell strainer (BD Falcon) and pelleted by centrifugation at 4000 g, 4°C for 5 min. After twice washing in buffer A1 at 4°C, the pellet was treated with 0.5 ml of complete lysis buffer (15 mM HEPES, pH 7.6; 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1%Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.1% SDS, 0.5 % N-lauroylsarcosine, Roche cOmplete protease inhibitor) and sonicated to break chromatin into fragments with an average length of  200-600 bp. The material was pelleted by centrifugation at 18 000 g for 5 min, and the supernatant fluid was transferred to a new tube. The pellet was treated with the second 0.5-ml portion of lysis buffer, and the preparation was centrifuged at 18 000 g for 5 min. The two portions of the supernatant fluid were pooled, cleared by centrifuging twice at 18 000 g for 10 min, and the resultant chromatin extract (1 ml) was used for ChIP experiments. 9 ml of ChIP dilution buffer (15 mM HEPES, pH 7.6; 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1%Triton X-100, 0.5 mM DTT, Roche cOmplete protease inhibitor), was added to the sheared chromatin together with 50 ul of prewashed Protein A Sepharose beads (GE Healthcare). The samples were incubated at 4 oC for 1 hour on a rotating platform. The samples were spun at 10,000g to remove the beads and the supernatant was transferred to a fresh tube. One aliquot (1/10 volume) of chromatin extract after preincubation with Sepharose was kept as a control sample (Input).
DNA concentration of 5ul was measured using a Qubit 3.0 fluorometer (Invitrogen). 1.5ng of starting material/sample was used to make each library. ChIP-seq libraries were obtained using the NEBNext Ultra™ II DNA library preparation kit (New England Biolabs) or with the Thruplex DNA-seq and single index kits (Takara) following the manufacturer’s instructions. Samples were sequenced by 50bp or 100bp single-end sequencing with HiSeq2500 (Illumina) or with NovaSeq6000 sequencer.

value: Wild-type

tag: antibody


title: circRNA DEF cells infected with NDV-3

status: Public on Apr 11 2023

city: Guangzhou

first: Lei

last: Fan

state: Guangdong

address: 483 Wushan Road,

country: China

institute: South China Agricultural University

data_processing:
Filtering of Clean Reads
Alignment with Ribosome RNA (rRNA) using short reads alignment tool Bowtie2
Alignment with Reference Genome by using  TopHat2
Identification of circRNA by using find_circ
Assembly: ncbi_GCF_003850225.1
Supplementary files format and content: excel format: Number of raw junction read

organism: Anas platyrhynchos

source_name: Duck embryo fibroblasts

extract_protocol:
1) Wash worms from a 60 mm plate with 1 ml DEPC-treated water.2) Spin down worms at 4000xg in microfuge for 1 minute.3) Remove excess water and add 1 ml Trizol reagent. Vortex and invert tube. Let sit at room termerature for 10 minutes (should see stringy-like material).4) Spin tubes in microfuge at 14K for 10 minutes at 4° C.5) Remove supernatant into fresh RNAse free eppendorf tube and add 200 µl of chloroform.6) Vortex for 15 seconds and let sit at room temperature for 3 minutes.7) Spin in microfuge at 12K for 15 minutes at 4° C.8) Carefully remove the top layer (clear) into a new RNAse free eppendorf tube and add 500 µl of Isopropanol. Invert to mix. Let sit for 10 minutes at room temperature.9) Spin in microfuge at 12K for 10 minutes at 4° C. (RNA will be seen as a nice white pellet).10) Wash pellet with 100 µl of 75% ethanol (made by diluting into DEPC-treated water).11) Spin in microfuge at 7500 xg for 5 minutes at 4° C.12) Remove supernatant and air dry pellet for 10 minutes.13) Dissolve pellet in 25 µl of DEPC-treated water. Heat for 10 minutes at 60° C to help dissolve RNA.
After extracted, total RNAs were treated with RNase R to degrade the linear RNAs, and purified using RNeasy MinElute Cleanup Kit（Qiagen）. Next, strand-specific library was constructed using VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina following the manufacture’s instructions. Briefly, ribosome RNAs were removed to retain circRNAs. The enriched circRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers. Second_x0002_strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with VAHTSTM DNA Clean Beads, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were purified with VAHTSTM DNA Clean Beads, PCR amplified, and sequenced using Illumina HiSeqTM 2500

value: Duck embryo fibroblasts

value: fibroblasts

value: WT

value: NDV infected (MOI = 1)

tag: time

value: 9 hpi


title: circRNA DEF cells infected with NDV-2

tag: cell type


title: N2 no treatment, replicate 1, scRNA-Seq

status: Public on Apr 12 2023

city: Charlottesville

first: Eyleen

last: O'Rourke

state: VA

address: 90 Geldard Dr

department: Department of Biology

institute: University of Virginia

description: 10x Genomics

data_processing:
The scRNA-Seq data was processed following the CellRanger pipeline. Reads were mapped to a modified version of the WormBase WS260 reference transcriptome that had transcript 3′ untranslated regions extended by 0 to 500 base pairs.
Assembly: Reads were mapped to a modified version of the WormBase WS260 reference transcriptome that had transcript 3′ untranslated regions extended by 0 to 500 base pairs.
Supplementary files format and content: pData (cell metadata) files for each biological replicate, fData (gene metadata) for each biological replicate, expression matrices for each biological replicates as RDS files.

organism: Caenorhabditis elegans

source_name: Whole worms

growth_protocol: Synchronized L1  N2 worms were grown at 20 degrees on HT115 bacteria for approximately 55h until they reached the young adult stage.

extract_protocol:
A synchronous population of L1 worms was obtained by double bleaching gravid N2 C. elegans with hypochlorite followed by 4 washes in S-buffer. The released eggs were then allowed to hatch in the absence of food in S-buffer over a period of 18 hours. Approximately 100,000 synchronized L1 worms were then grown in NGM plates seeded with HT115 bacteria at 20℃ for approximately 55h. 55h post-seeding, worms were staged under a microscope to ensure that they have reached the young adult stage. Young adult worms were then harvested in S-buffer and then centrifuged at 1,300g for 1 min. The worm pellet was washed until the suspension was no longer turbid (2-3 times) and then transferred to a 1.5mL Eppendorf tube. The cuticle was then disrupted by incubating the worms in 200μL SDS-DTT (20mM HEPES pH8.0, 0.25% SDS 200 mM DTT, 3% sucrose) for 4 minutes. Immediately after SDS-DTT treatment, 800 mL of egg buffer was added to the treated worms, the worms were centrifuged, the supernatant was aspirated and the worm pellet was washed 5 times in egg buffer (118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2, 25 mM HEPES, at osmolarity of 340 Osm). After the final wash, egg buffer was added to a final volume of 1mL and the worm solution was then transferred to a 15-mL conical tube. 500μL of 350 units/mL Pronase (EMD Millipore Corp) was added and the worms were then dissociated into single cells by passing them through a 21-gage needle about 20 times. The worm/cell lysate was centrifuged at 4℃ for 1 min at 200g and then most of the supernatant, containing dissociated cells, was transferred to a new 15-mL conical tube leaving behind enough liquid for a second round of dissociation. After passing the worm lysate through the needle for a second time, the samples were centrifuged (4℃ for 1 min at 200g) and then the supernatant was transferred to the same tube containing the cells from the first transfer. The cells were then centrifuged at 4℃ for 5 min at 500g and the cell pellet was washed 3 times in egg buffer containing 1% BSA gently pipetting the cells with wide-end tips. Finally, to separate single cells from bigger chunks of tissue, the cell suspension was gently passed through a 10μm filter.
For single cell capture, 14,000 C. elegans cells were mixed with the reverse transcriptase solution and then loaded onto each channel of the 10x Chromium Controller. The libraries were then built following the Chromium Next GEM Single Cell Kits v3.1 published protocols and then sequenced on an Illumina NextSeq 500 platform.

tag: tissue

value: Whole worms

tag: cell line

value: N2 wild type

value: no treatment


title: Disease plasma_PBMC_7_S7_L001

description: RNA bulk sequencing

value: peripheral blood mononuclear cells


title: N2 no treatment, replicate 3, scRNA-Seq

description: 10x Genomics

tag: genotype


title: N2 no treatment, replicate 2, scRNA-Seq

description: 10x Genomics


title: DEF cells infected with NDV-3

data_processing:
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis.
Alignment and Identification of small RNA in GeneBank and  Rfam database
Alignment with Genome (exon, intron, repeat sequences)
Identification of microRNA (miRNA) using  miRbase database and software Mireap_v0.2
Small RNA annotation summary and miRNA expression profiles
Assembly: ncbi_GCF_003850225.1
Supplementary files format and content: all_mirna.exp_profile.txt

extract_protocol:
1) Wash worms from a 60 mm plate with 1 ml DEPC-treated water.2) Spin down worms at 4000xg in microfuge for 1 minute.3) Remove excess water and add 1 ml Trizol reagent. Vortex and invert tube. Let sit at room termerature for 10 minutes (should see stringy-like material).4) Spin tubes in microfuge at 14K for 10 minutes at 4° C.5) Remove supernatant into fresh RNAse free eppendorf tube and add 200 µl of chloroform.6) Vortex for 15 seconds and let sit at room temperature for 3 minutes.7) Spin in microfuge at 12K for 15 minutes at 4° C.8) Carefully remove the top layer (clear) into a new RNAse free eppendorf tube and add 500 µl of Isopropanol. Invert to mix. Let sit for 10 minutes at room temperature.9) Spin in microfuge at 12K for 10 minutes at 4° C. (RNA will be seen as a nice white pellet).10) Wash pellet with 100 µl of 75% ethanol (made by diluting into DEPC-treated water).11) Spin in microfuge at 7500 xg for 5 minutes at 4° C.12) Remove supernatant and air dry pellet for 10 minutes.13) Dissolve pellet in 25 µl of DEPC-treated water. Heat for 10 minutes at 60° C to help dissolve RNA.
After total RNA was extracted by Trizol reagent kit (Invitrogen, Carlsbad, CA,USA), the RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel electrophoresis(PAGE). Then the 3’ adapters were added and the 36-44nt RNAs were enriched. The 5’ adapters were then ligated to the RNAs as well. The ligation products were reverse transcribed by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500

tag: developmental stage

value: embryo

tag: infection


title: circRNA Control of DEF cells-1

value: Non

value: 9 h


title: circRNA Control of DEF cells-3


title: circRNA Control of DEF cells-2


title: circRNA DEF cells infected with NDV-1


title: Healthy plasma_PBMC_14_S14_L001

description: RNA bulk sequencing


title: Healthy plasma_PBMC_12_S12_L001

description: RNA bulk sequencing


title: Immune_K2shControl_1

description: 10x Genomics (3' kit, v2.0)

value: sorted primary CD45+ immune cells

value: pancreas

value: KC;RIK-shIl33.668 (Off Dox)

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Il33 (sh668)

value: Caerulein / Day 2

value: 5-6 weeks old


title: Disease plasma_PBMC_10_S10_L001

description: RNA bulk sequencing

value: patient plasma stimulation


title: Control of DEF cells-3

value: fibroblasts

value: WT


title: DEF cells infected with NDV-1

value: NDV infected (MOI = 1)

value: 9 hpi


title: Control of DEF cells-1


title: Control of DEF cells-2


title: Healthy plasma_PBMC_11_S11_L001

description: RNA bulk sequencing

value: healthy donor plasma stimulation


title: Muscle, No training, Control 10

status: Public on Mar 26 2023

city: Albany

first: J

middle: Andrew

last: Berglund

address: 1400 Washington Avenue

department: RNA Institute, Life Sciences

institute: University at Albany

data_processing:
Quality of each fastq file was checked using FastQC v0.11.9
Both paired-end files for 2019 Pre-training sample were downsampled using Seqtk v1.3 to to a read depth comparable with the other samples (~60 million reads per paired-end file).
Fastq files were aligned to the hg38 using STAR v2.7.9 specifying --quantModeGeneConuts to obtain files containing raw gene expression abundance files.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files contain raw read count abundance files for each sample.
Supplementary files format and content: FPKM.csv: Comma-separated text file includes FPKM values for each Sample.
Supplementary files format and content: FastQC_Reports_GSE208639.pdf: File includes the FastQC report for each RNA-seq sample included in this study. These reports were generated using FastQC version 0.11.9. The FastQC_Reports_Sample_Numbers_GSE208639.xlsx file lists the corresponding GSM accession number for each sample referenced in the file.
Supplementary files format and content: GSE208639_rMATS_output: This file contains skipped exon (SE) event percent spliced in (PSI) and delta PSI values for each pre- or post-training individual as compared to controls held at baseline, as well as all pre- or post-training individuals grouped compared to controls. These values were generated using rMATS version 4.1.1.
Supplementary files format and content: GSE208639_edgeR_output: This file contains the log2FC change in expression values for each pre- or post-training individual as compared to controls held at baseline, as well as all pre- or post-training individuals grouped compared to controls. These values were generated using edgeR version 3.34.1 and p values were calculated in edgeR by a quasi-likelihood F-test.

source_name: Vastus lateralis

extract_protocol:
RNA was extracted using 1.5mm zirconium beads (MidSci) and Zymo Quick-DNA/RNA microprep plus kit (Zymo Research) with on-column DNase treatment. RNA quality was checked via capillary electrophoresis on a fragment analyzer using the RNA Analysis DNF-471 kit (Advanced Analytical).
The NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) with NEBNext rRNA Depletion Kit (New England Biolabs) was used to prepare RNA-seq libraries, with a total of at least 500 ng input RNA from each sample. The manufacturer’s protocols were followed, with the following exceptions: 40× adaptor dilutions were used, all bead incubations were done at room temp, a 4× lower concentration of index primers was used, and 10 cycles of library amplification were performed. The resulting libraries were pooled in equimolar amounts, quantified using the KAPA Library Quant Kit for Illumina (Kapa Biosystems), quality checked via capillary electrophoresis on the fragment analyzer using the NGS Analysis DNF-474 kit (Advanced Analytical), and were sequenced using paired-end, 75 base pair sequencing on the Illumina NextSeq 500 massively parallel sequencer at the University at Albany Center for functional genomics.

treatment_protocol: Following biopsies, muscles samples were immediately rinsed in a cold phosphate buffered saline solution (PBS) and frozen in tissue freezing medium in isopentane cooled in liquid nitrogen. The samples were then stored at −80 °C until further use.

value: Vastus lateralis

value: Unaffected control

value: No training


title: Muscle, No training, Control 4


title: Muscle, No training, Control 1


title: Muscle, No training, Control 11


title: Muscle, Pre-training, 1806

value: Pre-training


title: Muscle, No training, Control 2


title: Muscle, Post-training, 1806

value: Post-training


title: Muscle, Post-training, 2002


title: Muscle, Post-training, 1791


title: Muscle, No training, Control 13


title: Muscle, Post-training, 523


title: Muscle, Pre-training, 1791


title: Muslce, Post-training, 1242


title: Muscle, Pre-training, 523


title: Muscle, Pre-training, 1242


title: Muscle, Pre-training, 2005


title: Muscle, Post-training, 2005


title: Muscle, Post-training, 2110


title: Muscle, Pre-training, 2110


title: Muscle, Post-training, 907


title: DEF cells infected with NDV-2

value: embryo


title: Muscle, Pre-training, 907


title: Muscle, Post-training, 2019


title: Muscle, Pre-training, 2002


title: wt control 2

status: Public on Mar 21 2023

city: Boulder

first: Ben

last: Barthel

institute: Edgewise Therapeutics

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Individual sample counts were normalized via Relative Log Expression (RLE) using DESeq2 R library
Assembly: GRCm38
Supplementary files format and content: Tab separated values, matrix files, and comma-separated values

source_name: Gastrocnemius

extract_protocol:
Freshly dissected gastroc muscle was homogenized with homogenization buffer (10mM HEPES, 60mM KCl, 2mM EDTA, 0.5mM EGTA, 300mM sucrose, qH2O). The mixture was centrifuged for 10 minutes, resuspended in homogenization buffer, placed onto a discontinuous sucrose gradient (2.8M and 2.1M sucrose: 50mM HEPES, 25mM KCl, 5mM MgCl2, qH2O), and centrifuged for 3 hours at 4ºC. The interface was resuspended in resuspension buffer (20mM HEPES, 10mM KCl, 1.5mM MgCl2, 0.2mM EDTA, qH2O), centrifuged, and nuclei counted with BioRad TC20 Automated Cell Counter.
Library was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics)

value: Gastrocnemius

value: Vehicle


title: wt control 1

description: 10x Genomics


title: mdx treated 1

description: 10x Genomics

value: 3 mg/kg EDG-5506


title: Muscle, Pre-training, 2019


title: mdx treated 2

description: 10x Genomics


title: mdx treated 3

description: 10x Genomics


title: mdx control 1

description: 10x Genomics


title: Ac_HL_1455 rep 3 [12_3]

city: Grenoble

first: Dimitris

last: Petroutsos

address: 17 rue des Martyrs

country: France

institute: 4University of Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV

data_processing:
Adapter Sequences in raw-reads were trimmed using Bbduk v.38.82 (ktrim=r k=30 mink=12 minlen=50).
Reads were mapped to the C. reinhardtii reference genome (JGI v.5.6) using the STAR aligner v.2.5.3 with default parameters.
The obtained BAM files were analyzed using HTSseq-count v.0.11.1  ("stranded=reverse") to generate gene-wise raw count files.
Assembly: C. reinhardtii JGI v5.6
Supplementary files format and content: Tab-separated text file with raw counts from HTSseq output. Library names as column names and gene locus IDs as row names.

organism: Chlamydomonas reinhardtii

growth_protocol: C. reinhardtii strain CC-125 was grown under 15 µmol photons m-2 s-1 in Tris-acetate-phosphate (TAP) media at 23 oC in Erlenmeyer flasks shaken at 125 rpm.

extract_protocol:
Freshly obtained samples were lysed using Tri-reagent (Sigma). After double chloroform extraction the aqueous phase was transferred to a RNeasy Mini-Kit column (Quiagen) and processed according to the manufacturers guide.
TruSeq LT libraries stranded mRNA protocol

treatment_protocol: For RNA sampling cells were transferred to Sueoka's high salt medium (HSM) at 1 million cells mL-1, 5 µmol photons m-2 s-1. At timepoint 0 part of the culture was supplied with 20mM of acetate. After 240 min and 1440min part of the cultures with and without acetate were exposed to 300 µmol photons m-2 s-1, samples were taken after 15min and 60min of high light exposure. For the continuous low light cultures samples were taken 15min, 240min (before 1st high light treatment) and 1440min (before 2nd high light treatment) after acetate addition.

tag: culture media

value: HSM (20mM Acetate)

tag: timepoint (min)

tag: light irradiance_(photons_m^-2_s-^1)


title: Ac_HL_1455 rep 2 [12_2]


title: mdx control 3

description: 10x Genomics


title: mdx control 2

description: 10x Genomics


title: HSM_HL_1500 rep 1 [13_2]

value: HSM


title: HSM_HL_1500 rep 2 [13_3]


title: Ac_HL_1455 rep 1 [12_1]


title: HSM_HL_1455 rep 3 [11_3]


title: HSM_HL_1500 rep 3 [13_4]


title: Ac_HL_1500 rep 3 [14_4]


title: HSM_HL_1455 rep 2 [11_2]


title: HSM_HL_1455 rep 1 [11_1]


title: Ac_HL_1500 rep 2 [14_3]


title: Ac_HL_1500 rep 1 [14_2]


title: Ac_LL_1440 rep 2 [10_2]


title: Ac_LL_1440 rep 1 [10_1]


title: Ac_HL_300 rep 1 [8_2]


title: HSM_LL_1440 rep 1 [9_2]


title: Ac_HL_300 rep 2 [8_3]


title: Ac_HL_300 rep 3 [8_4]


title: HSM_LL_1440 rep 2 [9_3]


title: HSM_HL_300 rep 3 [7_4]


title: HSM_HL_300 rep 1 [7_1]


title: HSM_HL_300 rep 2 [7_3]


title: Ac_HL_255 rep 3 [6_4]


title: Ac_HL_255 rep 2 [6_3]


title: Ac_HL_255 rep 1 [6_2]


title: Ac_LL_1440 rep 3 [10_4]


title: HSM_HL_255 rep 2 [5_2]


title: HSM_LL_240 rep 2 [3_3]


title: Ac_LL_240 rep 1 [4_1]


title: Ac_LL_240 rep 3 [4_3]


title: HSM_LL_240 rep 3 [3_4]


title: HSM_HL_255 rep 1 [5_1]


title: Ac_LL_15 rep 2 [2_3]


title: HSM_LL_15 rep 1 [1_1]


title: HSM_LL_15 rep 2 [1_2]


title: HSM_LL_1440 rep 3 [9_4]


title: Ac_LL_15 rep3 [2_4]


title: Ac_LL_15 rep 1 [2_2]


title: D17-1

status: Public on Mar 08 2023

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

data_processing: For alignment and quantification of gene.tpm files we used the Whippet-quant function of Whippet v0.11. This aligns and quantifies in one step

growth_protocol: HeLa/HEK293T cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin (Invitrogen).

extract_protocol:
After 48-72h RNA was extracted using RNATri (Bio&Sell) followed by DNaseI digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transient transfection of siRNA or plasmids were performed using Rotifect (Carl Roth) according to the manufacturer’s instructions.

tag: batch


title: WT-1

tag: treatment


title: CTRL-2

value: CTRL


title: D7-2


title: D7-1


title: WT-2


title: HSM_HL_255 rep 3 [5_3]


title: CTRL-E3

source_name: HeLa

value: siCTRL


title: CTRL-E2


title: PRKRIP1-3


title: PRKRIP1-2


title: D17-2


title: Ac_LL_240 rep 2 [4_2]


title: HSM_LL_240 rep 1 [3_1]


title: HSM_LL_15 rep 3 [1_3]


title: CTRL-E1


title: PRKRIP1-1


title: SLU7-3


title: SLU7-1


title: CTRL-D2


title: CTRL-D1


title: GPATCH1-3


title: GPATCH1-2


title: GPATCH1-1


title: NKAP-3

value: NKAP


title: CTRL-1


title: NKAP-2


title: CTRL-C3


title: SMU1-2


title: SMU1-3


title: CTRL-C2


title: CTRL-C1


title: FAM50A-2


title: FAM50A-3


title: FAM50A-1


title: TLS1-1


title: SD2-3


title: SLU7-2


title: TLS1-2


title: SD2-2


title: CTRL-D3


title: siCTRL-B3


title: SD2-1


title: NKAP-1


title: siDgcr14-3


title: siCTRL-B1


title: siNosip-2

value: siNosip


title: siCTRL-B2


title: siNosip-3


title: siDgcr14-2


title: siDgcr14-1


title: siPpil3-3


title: siNosip-1


title: siPpil3-1


title: siPpil3-2


title: SMU1-1


title: siCXorf56-1


title: siFam32a-3


title: TLS1-3


title: siCXorf56-2


title: siCXorf56-3


title: siFam32a-2


title: siFam32a-1


title: siCTRL-3


title: siWDR70-2


title: siCTRL-1


title: siDHX35-1


title: siWDR70-3


title: siDHX35-3


title: siWDR70-1


title: siDHX35-2


title: siDDX41-2


title: siDDX41-3


title: siPPWD1-1


title: Naive CD4+ T cells, Control_Rep1

status: Public on Mar 05 2023

city: shanghai

first: bao

last: wang

address: jin zun road

institute: shanghai jiao tong university school of medicine

data_processing:
The sequencing data were aligned to the mouse reference genome (mm10) using the STAR aligner (version 2.7.3a). All mapped reads were subsequently counted using HTSeq (version 0.12.4).
Assembly: mm10
Supplementary files format and content: counts

source_name: spleens

extract_protocol: RNA-seq libraries were constructed by Anoroad (Beijing, China) using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (NR604-01/02) according to the manufacturer’s instructions.

treatment_protocol: Mice spleen were harvested and CD4+ naive T cells were enriched by magnetic beads followed by RNA-sequencing.

value: spleens

value: Naive CD4+ T cells

value: Control


title: siPPWD1-2


title: Naive CD4+ T cells, Control_Rep3


title: APP/PS1+MOX

status: Public on Feb 22 2023

city: Chendu

first: Qiaofeng

last: Wu

address: No. 37, Twelfth Bridge Road, Jinniu District

institute: Chengdu University of Traditional Chinese Medicine

data_processing:
Library strategy: Spatial Transcriptomics
bcl2fastq command line tool was used for base calling  Sequence reads were trimmed for adapter sequence and polyA homopolymers using cutadapt
Reads were mapped, annotated and demultiplexed using the spaceranger v1.0.0 command line tool
Annotated reads were quantified and mapped to the Hematoxylin and Eosin image using the spaceranger v1.0.0 command line tool
Assembly: mm10 (Ensembl 93)
Supplementary files format and content: raw.zip include matrix with raw counts for every gene and every spot and spatial informations

source_name: brain

extract_protocol:
The brains were coronally cryosectioned at a thickness of 10 μm by Cryostat Microtome (Leica CM3050, Germany). Then 5-10 sections were selected to be stained with HE, photographed and tested for RNA integrity number (RIN) value.
RNA libraries were prepared for sequencing following the 10x Genomics Visium protocol
Spatial Transcriptomics (Visium)

value: brain

value: male

value: 7 months of age

value: Moxibustion


title: APP/PS1


title: siCTRL-2


title: PPM1A_OE_Mtb_2 [ATAC-seq]

status: Public on Feb 08 2023

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Fasta sequence files were analyzed for quality using fastQC v0.11.9
ATAC-seq reads were trimmed using fastp v0.20.1 with the parameters --length_required 25, --cut_tail, --cut_tail_window_size 4, --cut_tail_mean_quality 20, --disable_quality_filtering.
ATAC-seq reads were aligned to the human hg38 genome using STAR v2.7.5a without gene annotation GTF file, with the parameters --alignIntronMax 1 --alignEndsType Extend5pOfReads12 --alignMatesGapMax 2000, --outFilterMatchNminOverLread 0.50, --outFilterScoreMinOverLread 0.50 and filtering for properly paired mates with a mapq score of 40 or above (Dobin et al. 2013) and duplicates were marked using Picard (Picard Tools).
ATAC-seq sequencing pairs were adjusted by +5 and -4 base pairs deepTools AlignmentSieve with parameter --ATACshift.
ATAC-seq peak calling was conducted separately on each replicate using MACS2 with q-value of 0.00001 cutoffs, and peaks within blacklisted regions were removed with BEDTools.
ATAC-seq consensus peaks (peaks that were found in at least two samples) were identified using rmspc.
ATAC-seq read ends overlapping consensus peaks were counted using RSubread featureCounts with parameters: isPairedEnd = FALSE, autosort=TRUE, countMultiMappingReads = FALSE,ignoreDup = FALSE, read2pos=5
Assembly: hg38
Supplementary files format and content: BED file describing consensus peak locations; text file with read end counts over consensus peaks

growth_protocol: RPMI 1640, 10% heat-inactivated fetal bovine serum, 2 mM glutamine, 10 mM HEPES, 100 I.U./ml  penicillin, μg/ml streptomycin.  Cells were cultured at 37°C at 5% CO2.

extract_protocol:
Cells were lysed with buffer containing 0.15 NP-40, 0.1% Tween-20 and 0.01% digitonin and incubated on ice for 3 min.  After cell lysis, nuclei were pelleted for 10 min at 4º C in a fixed angle centrifuge.
ATAC-seq libraries were prepared using Transposition mix (2X Tagmentation DNA buffer (20 mM Tris-HCl, 10 mM MgCl2, 20% dimethyl formamide), 3.5 µl transposase, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 4 µl H2O) made in-house. Libraries were cleanued up individually using Qiagen MinElute PCR purification kits. Transposed DNA libraries were amplified for 4-8 cycles using NEBNext High-Fidelity 2X PCR Master Mix and amplified using unique dual barcoding primers. PCR amplification reactions were purified using MagBio HighPrep PCR clean up kits to remove DNA fragments less than 50 bp and greater than 1000 bp.

treatment_protocol:
THP-1 monocytes were differentiated with 100 ng/ml phorbol ester 13-phorbol-12-myristate acetate (PMA) for 72 h.
THP-1 cells were infected with Mtb mc26206 growing in log-phase at a multiplicity of infection (MOI) of 10 for 16 h. Extracellular, non-phagocytosed bacteria were removed by three phosphate buffered saline (PBS) washes. Infection was continued at 37°C for a total infection time of 48 h.

value: Macrophage

value: PPM1A overexpression

value: Mtb infection


title: PPM1A_OE_Mtb_3 [ATAC-seq]


title: PPM1A_KO_Mtb_2 [ATAC-seq]

value: PPM1A knockout


title: WT_Mtb_2 [ATAC-seq]

value: WT


title: PPM1A_OE_NI_2 [ATAC-seq]


title: PPM1A_KO_Mtb_3 [ATAC-seq]


title: WT_Mtb_3 [ATAC-seq]


title: PPM1A_OE_NI_3 [ATAC-seq]


title: PPM1A_KO_NI_3 [ATAC-seq]


title: PPM1A_KO_NI_2 [ATAC-seq]


title: WT_NI_3 [ATAC-seq]


title: PPM1A OE_Mtb_4

data_processing:
RNA-seq sequence reads were trimmed using fastp v0.20.1 with the parameters --length_required 25,  --cut_tail, cut_tail_window_size 4, --cut_tail_mean_quality 20, --disable_quality_filtering, --overrepresentation_analysis
Filtered reads were aligned to the human hg38 genome using STAR v2.7.5a, with the parameters --outReadsUnmapped Fastx, --outFilterMatchNminOverLread 0.50, --outFilterScoreMinOverLread 0.50 --outSAMmapqUnique 40, --outFilterMultimapNmax 1 and duplicate reads were marked with Picard  (Picard Tools).
Subread featureCounts was used to assign reads to gene exons and to summarize counts at the gene level. Represented genes were annotated using biomaRt.
Assembly: hg38
Supplementary files format and content: RNA-seq read counts over exons and summarized over genes

growth_protocol: RPMI 1640, 10% heat-inactivated fetal bovine serum, 2 mM glutamine, 10 mM HEPES, 100 I.U./ml  penicillin, μg/ml streptomycin  Cells were cultured at 37°C at 5% CO2.

extract_protocol:
RNA was harvested using Aurum™ Total RNA Mini Kit (Bio-Rad) as per the manufacturer’s protocols. All samples were incubated in lysis buffer for 20 minutes to inactivate bacteria in Mtb-infected samples.
cDNA libraries were generated from mRNA samples with the NEB Ultra II Directional polyA mRNA library prep kit for Illumina.


title: WT_Mtb_4


title: PPM1A KO_Mtb_4


title: PPM1A KO_NI_4


title: Naive CD4+ T cells, Control_Rep2


title: WT_NI_4


title: PPM1A OE_Mtb_3


title: siDDX41-1


title: WT


title: PPM1A OE_Mtb_2


title: siPPWD1-3


title: PPM1A KO_Mtb_3


title: PPM1A KO_Mtb_2


title: PPM1A OE_NI_3


title: WT_Mtb_2


title: PPM1A KO_NI_3


title: PPM1A OE_NI_2


title: WT_NI_2


title: WT_NI_2 [ATAC-seq]


title: NC MBD3 R1 IgG

status: Public on Feb 02 2023

city: Xi'an

first: Jian

last: MA

state: Shan Xi

address: West Yanta road 227

institute: The First Affiliated Hospital of Xi'an Jiaotong University

data_processing:
The size distribution of libraries was determined by Agilent 4200 TapeStation analysis, and libraries were mixed to achieve equal representation as desired aiming for a final concentration as recommended by the manufacturer. Sequencing was performed in the Illumina Novaseq 6000 using 150bp paired-end following the manufacturer’s instructions.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Peaks were annotated by using homer's annotatePeaks.pl.
Assembly: hg38
Supplementary files format and content: each sample include an IgG.bw file and a sample.bw file
Supplementary files format and content: the raw data contain paired IgG.fq.gz and sample.fq.gz files

source_name: prostate

growth_protocol: PC-3 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
100000 cells were washed twice with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). 10 μL Concanavalin A coated magnetic beads (Bangs Laboratories) were added per sample and incubated at RT for 10min. The unbound supernatant were removed and the bead-bound cells were resuspended with Dig-wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2 mM EDTA) and incubated with a 1:50 dilution of primary antibody or IgG control antibody on a roating platform overnight at 4℃. Secondary antibody (Rabbit Anti-Mouse IgG H&L: abcam, ab611709; Anti-Rabbit IgG antibody, Goat monoclonal: Millipore AP132) was diluted 1:100 in Dig-wash buffer and cells were incubated at RT for 60 min. A 1:100dilution of pA-Tn5 adapter complex was prepared in Dig-med buffer (0.01% Digitonin; 20 mM HEPES pH 7.5; 300 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail) and incubated with cells at RT for 1h. Then cells were resuspended in tagmentation buffer (10 mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
To amplify libraries, 21 μL DNA was mixed with 2 μL of a universal i5 and barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C.
Cleavage Under Targets and Tagmentation (CUT&Tag)

treatment_protocol: PC-3 cells were treated with or without IR (5Gy)

value: prostate

value: prostate cancer cell line


title: WT_NI_3


title: PPM1A KO_NI_2


title: IR LSD1 R1 IgG

value: IR


title: NC MBD3 R2 IgG


title: PPM1A OE_NI_4


title: IR MBD3 R1 IgG


title: IR MBD3 R2 IgG


title: IR LSD1 R2 IgG


title: NC LSD1 R1 IgG


title: MBD3 IR R2


title: NC LSD1 R2 IgG


title: MBD3 IR R1


title: MBD3 NC R2


title: WT_Mtb_3


title: MBD3 NC R1


title: LSD1 IR R1


title: LSD1 IR R2


title: LSD1 NC R1


title: LSD1 NC R2


title: LLC cells, BAY-876 (36h), rep2

status: Public on Jan 18 2023

city: Beijing

first: Lijian

state: Beijing

address: 30 Shuangqing Rd, Haidian District, Beijing

department: School of Medicine

institute: 清华大学

data_processing:
STAR v2.6.1d, Salmon v0.14.1, tximport v1.22.0, DESeq2 v1.34.0
RNA-seq reads were aligned to mm10 genome vM25 using STAR v2.6.1d.
Read alignments were quantified by Salmon v0.14.1 in its alignment-based mode.
Gene-level counts from quantification files were prepared for normalization and differential expression analysis with tximport v1.22.0.
Normalization and differential expression analysis were performed by DESeq2 v1.34.0 with default parameters.
Assembly: mm10
Supplementary files format and content: comma-delimited csv files include DESeq2 normalized values for each Sample

source_name: LLC

growth_protocol: LLC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LLC cells were treated with 200 nM BAY-876 or vihicle control for 36 hours.

value: LLC


title: LLC cells, BAY-876 (36h), rep1


title: LLC cells, Vehicle (36h), rep2

value: Vehicle


title: LLC cells, Vehicle (36h), rep1


title: LLC cells, BAY-876 (36h), rep3


title: AGS TK+ c1

status: Public on Jan 09 2023

city: New Haven

first: Jason

last: Sheltzer

state: CT

address: 300 George Street

department: Surgery

institute: Yale University

description: Gastric adenocarcinoma cell line, harboring gain of chr1q and TK+ integrant

data_processing:
Custom Novogene QC scripts
Novogene: Remove reads containing adapters
Novogene: Remove reads containing >10% undetermined bases (N)
Novogene: Remove reads with >=50% of bases with Qscore <= 5
Hisat2 (v2.0.5) alignment to hg38
featureCounts v1.5.0-p3 to count reads mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: AGS

growth_protocol: Cells were plated and allowed to grow for 24 hours prior to extraction

extract_protocol:
Qiagen RNEeasy
In brief, mRNA was purified from total cellular RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis. Subsequently, libraries were prepared with end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Single cell derived clones with engineered chr losses were generated through a collection of ReDACT techniques

value: AGS

value: gastric cancer

value: TK+

value: TK+ integrant


title: AGS TK+ c2


title: AGS 1q-loss c11

description: Gastric adenocarcinoma cell line with engineered loss of chr1q trisomy

value: ReDACT-CO, targeting chr1q


title: AGS 1q-loss c7

value: ReDACT-NS, targeting chr1q


title: AGS WT

description: Gastric adenocarcinoma cell line, harboring gain of chr1q

value: Wildtype


title: AGS 1q-loss c4


title: HCT116 8q-loss c2 rep 2

description: Colorectal cancer cell line with engineered loss of chr8q trisomy

value: colorectal cancer

value: ReDACT-CO, targeting chr8q


title: HCT116 WT rep 1

description: Wildtype colorectal cancer cell line, harboring gain of chr8q


title: AGS 1q-loss c1


title: AGS 1q-loss c6


title: HCT116 WT rep 2


title: HCT116 8q-loss c1 rep 2


title: HCT116 8q-loss c1 rep 1


title: A2058 7p-loss c3 rep 2

description: Melanoma cell line with engineered loss of chr7p trisomy

value: melanoma

value: ReDACT-CO, targeting chr7p


title: A2058 7p-loss c3 rep 1


title: HCT116 8q-loss c2 rep 1


title: A2058 WT rep 1

description: Wildtype melanoma cell line, harboring gains of chr1q, 7p, and 8q

value: WT


title: A2058 WT rep 2


title: A2058 7p-loss c2 rep 2


title: LLC cells, Vehicle (36h), rep3


title: A2058 1q-loss c1 rep 2

description: Melanoma cell line with engineered loss of chr1q trisomy


title: A2058 7p-loss c1 rep 1


title: A2058 1q-loss c2 rep 2


title: A2058 1q-loss c1 rep 1


title: A2058 7p-loss c1 rep 2


title: A2058 1q-loss c2 rep 1


title: A2058 7p-loss c2 rep 1


title: A2058 WT rep 3


title: A2058 8q-loss c1 rep 1

description: Melanoma cell line with engineered loss of chr8q trisomy


title: A2058 8q-loss c2 rep 1