title: nodrug-rna-3

status: Public on Aug 05 2023

city: San Antonio

first: David

last: Kadosh

state: Texas

address: 7703 Floyd Curl Dr., MC: 7758

department: Department of Microbiology, Immunology & Molecular Genetics

description: NoDrug RNA-seq replicate 3

data_processing:
Adaptor sequences and low-quality score (phred quality score < 5) bases were trimmed from RNA-Seq and Ribo-Seq datasets with TrimGalore (v 0.4.3) (Krueger, 2012). Only reads that were at least 20 nucleotide long were retained.
Trimmed sequences from RNA-seq and Ribo-seq were both mapped using STAR (v.2.5.2b) (Dobin, 2013) using Assembly 22 fasta as the reference and GTF s07-m01-r27 from CGD allowing a mismatch of at most two positions (--outFilterMismatchNmax 2). Only uniquely mapping reads were retained (-outFilterMultimapNmax 1). All the reads mapping to non-mRNA sequences were filtered out before downstream analysis. The corresponding non-mRNA sequences were also obtained from CGD (C_albicans_SC5314_version
_A22-s07-m01-r27_other_features_no_introns.fasta). The periodicity analysis of Ribo-seq data was performed using ribotricer (v1.3.2) (Choudhary, 2020). Gene level counting was performed using featureCounts (v1.6.4) (Liao, 2014). Since Assembly 22 is a diploid assembly, the reads were counted for each copy of the gene separately (hapA and hapB) and then merged into a single read count per gene.
Differential expression analysis was performed using DESeq2 (Love, et al, 2014). Only genes with at least one read per replicate were selected for performing the library size normalization step and running the moderated t-statistic test. Genes were defined to be differentially expressed (DE) if the transcripts per million (TPM) was greater than 1 in at least 3 replicates and if their absolute fold-change on log2 scale is at least 1 with an FDR adjusted p-value of less than or equal to 0.05.
Differential translational efficiency was performed using riborex (Li, 2017) by retaining genes that had at least one read count in one replicate across the two conditions in both Ribo-seq and RNA-seq samples. Only genes that had a read count of at least one per replicate were used as input to riborex. We define genes to be exhibiting differential translational efficiency if their TPM was greater than 1 in at least 3 replicates while the absolute fold-change on log2 scale was at least 1 and the corresponding non-adjusted p-value less than or equal to 0.05. Gene ontology (GO) analysis was performed using clusterProfiler (Yu, 2012) using GO slim ontology file available from CGD.
Assembly: ASM18296v3
Supplementary files format and content: raw counts table

organism: Candida albicans

source_name: fungal cells

growth_protocol: For ribosome profiling experiments, a saturated overnight culture of C. albicans wild-type strain SC5314 was grown in YEPD (yeast extract‐peptone‐dextrose) medium at 30°C and 200 rpm.  The culture was diluted in 50 mL YEPD medium and incubated until reaching an OD600 of 1.0. The culture was further diluted to an OD600 of 0.025 in 400 mL fresh YEPD and grown to OD600 = 0.050. At this point 200 mL of culture was transferred to two 1 L flasks.

extract_protocol:
Cells were recovered by filtration at room temperature, rapidly scraped off the filter paper with a cell scraper, placed into ice-cold lysis buffer (1x yeast polysome buffer (Illumina), 1% Triton X-100 (Sigma), 50 ug/mL GMPPNP (Sigma), 10 ug/mL Blasticidin S (InvivoGen)), and  homogeneously mixed, followed by snap freezing in liquid nitrogen. Cell lysates were prepared and ribosome profiling was performed using four biological replicates as we have described previously (Mundodi, et al., G3 11(2):jkaa043 (2021)).
Ribosome profiling and library preparation were carried out according to the protocol described for the True Seq Ribo Profile (Yeast) Kit (Illumina). Lysates were digested with 15 U RNase I (Ambion) per A260 unit and incubated at room temperature for 45 min. with gentle rotation. The reactions were stopped by the addition of 1000U/mL SUPERase-IN (Ambion). 80S monosome fractions were purified from the cell lysate using MicroSpin S-400 HR columns (GE Healthcare). Ribosome protected fragments (RPFs) were further purified using the RNA Clean & Concentrator-25 Kit (Zymo Research) method. This kit was also used for total RNA purification. rRNA depletion was carried out using a Ribo-Zero Magnetic Gold (Yeast) kit (Illumina). An additional subtraction step was included to remove rRNA sequences from circularized cDNA as described previously (Spealman et al. 2016) with slight modifications. Subtractions were carried out in a 30 uL reaction volume, with 10 uL sample, 2 uL 20X SSC and 2 uL of a rRNA subtraction pool containing custom-designed biotinylated oligonucleotides (see Dataset S8 in Mundodi, et al., G3 11(2):jkaa043 (2021)). The circularized DNA was next used as a template for amplification of library PCR products. PCR products of 140-160 bp were recovered from excised gel slices, quantified by Agilent Bioanalyzer/Fragment analyzer and deep sequencing was performed using an Illumina Hiseq3000 machine at the Greehey Children’s Cancer Research Institute Genome Sequencing Facility (University of Texas Health Science Center at San Antonio). All ribosome profiling experiments were performed in biological quadruplicate.

treatment_protocol: Fluconazole was added to one flask at 1 ug/mL and an equivalent volume of DMSO was added to the second flask as a vehicle only control. Both flasks were incubated at 30°C for 6 hours, which we had previously determined as the fluconazole IC50.  To confirm that a 50% reduction in cell count occurred due to fluconazole treatment, OD600 of both cultures was measured and compared.

value: fungal cells

tag: fraction

value: total RNA

tag: agent


title: Adult rep1

status: Public on Aug 28 2023

type: SRA

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

country: USA

institute: University of Connecticut School of Medicine

library_source: transcriptomic

data_processing:
Sequence reads were mapped to the mm10 genome and transcriptome by Hisat2 and transcripts quantified using the Cufflinks/cuffdiff pipeline
Reads mapping to the loci for Rpl7 and Rpl7a were extracted in BAM file format using SamTool 1.9
Assembly: mm10
Supplementary files format and content: csv file include FPKM values for Rpl7 from Cuffdiff for all samples

molecule: total RNA

organism: Mus musculus

source_name: RGCs

extract_protocol:
Embryonic day18, postnatal day 5 and 8 weeks adult RGCs were purified by immunopanning for Thy1 (after immunopanning depletion of macrophages and amacrine cells)
cDNA libraries prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina), paired reads sequenced 100 bp from each end on HiSeq 2000 Sequencer (Illumina).

tag: strain

tag: developmental stage

value: Adult

tag: cell type

value: RGCs

tag: genotype

value: WT


title: P5 rep2


title: nodrug-rna-2

institute: University of Texas Health Science Center at San Antonio

description: NoDrug RNA-seq replicate 2


title: E18 rep1


title: nodrug-rna-4

description: NoDrug RNA-seq replicate 4


title: nodrug-ribo-4

description: NoDrug Ribo-seq replicate 4

data_processing:
Adaptor sequences and low-quality score (phred quality score < 5) bases were trimmed from RNA-Seq and Ribo-Seq datasets with TrimGalore (v 0.4.3) (Krueger, 2012). Only reads that were at least 20 nucleotide long were retained.
Trimmed sequences from RNA-seq and Ribo-seq were both mapped using STAR (v.2.5.2b) (Dobin, 2013) using Assembly 22 fasta as the reference and GTF s07-m01-r27 from CGD allowing a mismatch of at most two positions (--outFilterMismatchNmax 2). Only uniquely mapping reads were retained (-outFilterMultimapNmax 1). All the reads mapping to non-mRNA sequences were filtered out before downstream analysis. The corresponding non-mRNA sequences were also obtained from CGD (C_albicans_SC5314_version
_A22-s07-m01-r27_other_features_no_introns.fasta). The periodicity analysis of Ribo-seq data was performed using ribotricer (v1.3.2) (Choudhary, 2020). Gene level counting was performed using featureCounts (v1.6.4) (Liao, 2014). Since Assembly 22 is a diploid assembly, the reads were counted for each copy of the gene separately (hapA and hapB) and then merged into a single read count per gene.
Differential expression analysis was performed using DESeq2 (Love, et al, 2014). Only genes with at least one read per replicate were selected for performing the library size normalization step and running the moderated t-statistic test. Genes were defined to be differentially expressed (DE) if the transcripts per million (TPM) was greater than 1 in at least 3 replicates and if their absolute fold-change on log2 scale is at least 1 with an FDR adjusted p-value of less than or equal to 0.05.
Differential translational efficiency was performed using riborex (Li, 2017) by retaining genes that had at least one read count in one replicate across the two conditions in both Ribo-seq and RNA-seq samples. Only genes that had a read count of at least one per replicate were used as input to riborex. We define genes to be exhibiting differential translational efficiency if their TPM was greater than 1 in at least 3 replicates while the absolute fold-change on log2 scale was at least 1 and the corresponding non-adjusted p-value less than or equal to 0.05. Gene ontology (GO) analysis was performed using clusterProfiler (Yu, 2012) using GO slim ontology file available from CGD.
Assembly: ASM18296v3
Supplementary files format and content: raw counts table
Library strategy: Ribo-seq

value: ribo


title: E18 rep2


title: nodrug-rna-1

description: NoDrug RNA-seq replicate 1


title: nodrug-ribo-3

description: NoDrug Ribo-seq replicate 3


title: fluconazole-rna-3

description: Fluconazole treated RNA-seq replicate 3

value: Fluconazole


title: fluconazole-rna-4

description: Fluconazole treated RNA-seq replicate 4


title: fluconazole-rna-2

description: Fluconazole treated RNA-seq replicate 2


title: fluconazole-ribo-4

description: Fluconazole treated Ribo-seq replicate 4


title: Cor-15 FSK-3

status: Public on May 13 2023

city: Singapore

first: Meng

last: Liu

state: Singapore

address: 11 Mandalay road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

data_processing:
Sequenced reads were aligned to the Hg19 human genome (GRCh37) with STAR version 2.5.2a
Cuffnorm version 2.2.1 was used to obtain quartile normalize fragments per kilobase per million reads (FPKM) expression matrix of genes across all samples.
Assembly: Hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: ARPKD patient-derived iPSCs

growth_protocol: Kidney organoids were generated based on the Low et al., 2019 Cell stem cell protocol

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 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: Kidney organoids were treated with DMSO or Forskolin for 3 days

tag: cell line

value: ARPKD patient-derived iPSCs

value: kidney organoid

value: PKHD1 mutation

tag: treatment

value: Forskolin

tag: time

value: 3 days


title: Cor-15 FSK-2


title: fluconazole-ribo-2

description: Fluconazole treated Ribo-seq replicate 2


title: fluconazole-ribo-1

description: Fluconazole treated Ribo-seq replicate 1


title: Cor-15 DMSO-2

value: DMSO


title: Cor-15 FSK-1


title: Cor-15 DMSO-3


title: Cor-15 DMSO-1


title: Epi-17 FSK-3

status: Public on May 08 2023


title: Epi-17 FSK-2


title: Epi-17 FSK-1


title: nodrug-ribo-2

description: NoDrug Ribo-seq replicate 2


title: Epi-17 DMSO-2


title: PTEN KD Regenerating RGCs

status: Public on Apr 11 2023

library_source: transcriptomic single cell

data_processing:
The plate-based generated scRNA-seq dataset (Pten KD regenerating RGCs) was merged with the 10X single cell platform generated scRNA-seq datasets (embryonic, adult atlas, and adult injured RGCs) using SAVER61, with default parameters for the plate-based generated scRNA-seq, for the downstream comparative analyses between the datasets. All datasets were normalized using Seurat’s NormalizeData function with default parameters. The sex-specific genes, Xist, Eif2s3y, Ddx3y, were excluded for dimensionality reduction but retained for downstream analyses. Embryonic and adult RGCs were aligned using the mutual nearest neighbors algorithm from Batchelor as part of the Monocle v.3, which was used to generate the merged embryonic and adult atlas RGC UMAP. Monocle was used to determine the pseudotime structure of the merged (embryonic/adult RGC) UMAP. The UMAP cell embeddings, generated by Monocle, were transferred to a Seurat object containing the same datasets, and the hyperparameters (umap.n.neighbors = 10; umap.metric = “euclidean”; umap.min.dist = 0.1; n_epochs = 200; learning_rate = 1; repulsion_strength = 1; negative_sample_rate = 5; approx._pow = 0; spread = 1) were used to generate a Seurat UMAP model. CellTools’ MapTo function was used to map the Pten KD regenerating RGCs to their cell type origins, and the injured and Pten KD regenerating RGCs were individually assigned the same pseudotime score as their nearest reference neighbor.
Assembly: mm10
Supplementary files format and content: CSV file contains PTEN knockdown regenerating RGCs normalized gene expression values for each cell

source_name: Retina

extract_protocol: Custom designed Drop-Seq barcodes from Integrated DNA Technologies (IDT) were delivered into wells of two 384-well plates. All primers in one well shared the same unique cell barcode and billions of different unique molecular identifiers (UMIs). Following cDNA synthesis, the contents of each well were collected and pooled into one tube using a Caliper SciClone Liquid Handler. After treatment with exonuclease to remove unextended primers, the cDNA was PCR amplified for 13 cycles and the cDNA was fragmented and amplified for sequencing using a Nextera XT DNA sample prep kit (Illumina).

tag: tissue

value: Retina

value: Retinal Ganglion Cell

value: PTEN Knowkdown and 2 weeks after crush injury


title: Epi-17 DMSO-3


title: P5_rep1

status: Public on Apr 10 2023

data_processing:
Sequence reads were mapped to the mm10 genome and transcriptome by Hisat2 and transcripts quantified using the Cufflinks/cuffdiff pipeline
Reads mapping to the loci for Crmp1, Crmp4 and Crmp5 were extracted in SAM file format using SamTool 1.9
Assembly: mm10
Supplementary files format and content: csv file include FPKM values for Crmp from Cuffdiff for all samples

molecule: polyA RNA

extract_protocol: cDNA libraries prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina), paired reads sequenced 100 bp from each end on HiSeq 2000 Sequencer (Illumina).

tag: strains

tag: age


title: nodrug-ribo-1

description: NoDrug Ribo-seq replicate 1


title: Adult_rep1


title: E18_rep2


title: P5_rep2


title: Epi-17 DMSO-1


title: fluconazole-ribo-3

description: Fluconazole treated Ribo-seq replicate 3


title: control_opticnerveccells

status: Public on Mar 27 2023

data_processing:
Illumina base-call files (*.bcl) were converted to FASTQs using CellRanger v1.3, which uses bcl2fastq v2.17.1.14. FASTQ files were then aligned to mm10 mouse reference genome and transcriptome using the CellRanger v1.3 software pipeline with default parameters which demultiplexes the samples and generates a gene versus cell expression matrix based on the barcodes and assigned unique molecular identifiers (UMIs) that enable determining the individual cells from which each RNA molecule originated.
For determining gene expression, normalization of the raw counts was performed using Seurat (v. 4.0.3) function, which divides the feature counts by the number of counts per each cell and then applies natural log transformation, resulting in normalized expression (NE) values.
Assembly: mm10

source_name: Mus musculus (P56);129S1/SvlmJ strain

extract_protocol: The amplified cDNA from each channel of the Chromium System was used to construct an Illumina sequencing library and sequenced on HiSeq 4000 with 150 cycle sequencing.

value: optic nerve

tag: Sex

value: pooled male and female

value: Wildtype

value: 2 weeks after crush


title: E18_rep1

value: RGCs


title: crushed_opticnervecells

source_name: Mus musculus (P56); 129S1/SvlmJ strain


title: fluconazole-rna-1

description: Fluconazole treated RNA-seq replicate 1

value: fungal cells

value: total RNA


title: COVIRS_102_22-00666_V3A

status: Public on Jan 12 2023

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: Total RNA sequenced from adult blood as part of the COVIRS study to investigate responses to vaccination

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Assembly: GRCh38
Supplementary files format and content: FeatureCounts per gene counts

source_name: Peripheral blood

extract_protocol: RNA extraction and genomic DNA elimination was carried out using the RiboPure RNA Purification kit for blood (Invitrogen) as per the manufacturer's instructions. Final elution into 50 uL RNase-free water. A further RNA precipitation reaction was carried out. RNA was resuspended 2.5x in 100% ethanol and 10% sodium acetate (Merck) and spun at 12,000 x g for 15 min at 4°C. Samples were washed in 75% ethanol. Pellets were air dried and resuspended in 29 uL RNase free water and total RNA yield was determined by analysis of samples using a TapeStation (Agilent, Santa Clara, USA) and Qubit (ThermoFisher Scientific, Waltham, USA). Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNASeq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer's instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix, targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD), was used to deplete these transcripts. The final library pool was converted to an MGI compatible circularized template using the MGIEasy Universal Library Conversion Kit (MGI, Shenzhen, China) before sequencing of the library pool (2 × 150 bp paired-end reads) was performed on an MGI DNBSEQ-G400.

value: Female

tag: timepoint

tag: first/second vaccine

tag: third vaccine

tag: run

tag: sample number


title: COVIRS_57_22-00662_V0


title: COVIRS_95_22-00667_V0

value: Missing


title: COVIRS_78_22-00668_V0


title: COVIRS_26_22-00659_V0


title: COVIRS_27_22-00660_V0


title: COVIRS_65_22-00310_V0


title: COVIRS_102_22-00312_V0


title: COVIRS_45_22-00309_V0

value: Male


title: COVIRS_44_22-00308_V0


title: COVIRS_42_22-00307_V0


title: COVIRS_100_22-00301_V3A


title: COVIRS_101_22-00302_V3A


title: COVIRS_18_22-00306_V0


title: Adult_rep2

value: Adult

value: WT


title: COVIRS_14_22-00303_V0


title: COVIRS_91_22-00299_V3A


title: COVIRS_96_22-00296_V3A


title: COVIRS_15_22-00304_V0


title: COVIRS_90_22-00298_V3A


title: COVIRS_93_22-00295_V3A


title: COVIRS_97_22-00297_V3A


title: COVIRS_27_22-00290_V1


title: COVIRS_89_22-00294_V3A


title: COVIRS_26_22-00289_V1


title: COVIRS_102_22-00288_V1


title: COVIRS_65_22-00286_V1


title: COVIRS_94_22-00285_V1


title: COVIRS_57_22-00292_V1


title: COVIRS_44_22-00283_V1


title: COVIRS_17_22-00280_V1


title: COVIRS_45_22-00284_V1


title: COVIRS_42_22-00282_V1


title: COVIRS_15_22-00279_V1


title: COVIRS_18_22-00281_V1


title: COVIRS_17_22-00305_V0


title: COVIRS_99_22-00300_V3A


title: COVIRS_64_22-00267_V3A


title: COVIRS_54_22-00265_V3A


title: COVIRS_73_22-00273_V3A


title: COVIRS_72_22-00272_V3A


title: COVIRS_70_22-00271_V3A


title: COVIRS_68_22-00270_V3A


title: COVIRS_14_22-00278_V1


title: COVIRS_78_22-00275_V3A


title: COVIRS_87_22-00277_V3A


title: COVIRS_66_22-00269_V3A


title: COVIRS_53_22-00264_V3A


title: COVIRS_65_22-00268_V3A


title: COVIRS_49_22-00263_V3A


title: COVIRS_77_22-00274_V3A


title: COVIRS_58_22-00266_V3A


title: COVIRS_43_22-00259_V3A


title: COVIRS_44_22-00260_V3A


title: COVIRS_36_22-00255_V3A


title: COVIRS_47_22-00262_V3A


title: COVIRS_42_22-00258_V3A


title: COVIRS_18_22-00252_V3A


title: COVIRS_86_22-00276_V3A


title: COVIRS_22_22-00253_V3A


title: COVIRS_16_22-00250_V3A


title: COVIRS_15_22-00249_V3A


title: COVIRS_17_22-00251_V3A


title: COVIRS_14_22-00248_V3A


title: COVIRS_12_22-00247_V3A


title: COVIRS_45_22-00261_V3A


title: COVIRS_99_V1_21-02004

tag: vaccine

value: Run 2


title: COVIRS_7_22-00246_V3A


title: COVIRS_25_V2A_21-01991


title: COVIRS_97_V0_21-01995


title: COVIRS_92_V1_21-02001


title: COVIRS_97_V1_21-02003


title: COVIRS_92_V0_21-01992


title: COVIRS_104_V0_21-02000


title: COVIRS_28_22-00254_V3A


title: COVIRS_101_V1_21-02006


title: COVIRS_94_V0_21-01994


title: COVIRS_99_V0_21-01996


title: COVIRS_93_V0_21-01993


title: COVIRS_24_V2A_21-01990


title: COVIRS_20_V2A_21-01988


title: COVIRS_93_V1_21-02002


title: COVIRS_103_V0_21-01999


title: COVIRS_8_V2A_21-01986


title: COVIRS_37_V1_21-01984


title: COVIRS_24_V1_21-01981


title: COVIRS_16_V2A_21-01987


title: COVIRS_35_V1_21-01983


title: COVIRS_38_V1_21-01985


title: COVIRS_22_V1_21-01980


title: COVIRS_100_V1_21-02005


title: COVIRS_100_V0_21-01997


title: COVIRS_91_V0_21-01979


title: COVIRS_90_V0_21-01978


title: COVIRS_101_V0_21-01998


title: COVIRS_22_V2A_21-01989


title: COVIRS_89_V0_21-01977


title: COVIRS_62_V2A_21-01973


title: COVIRS_86_V0_21-01974


title: COVIRS_88_V0_21-01976


title: COVIRS_53_V2A_21-01969


title: COVIRS_25_V1_21-01982


title: COVIRS_49_V2A_21-01967


title: COVIRS_56_V2A_21-01971


title: COVIRS_46_V2A_21-01966


title: COVIRS_54_V2A_21-01970


title: COVIRS_51_V2A_21-01968


title: COVIRS_38_V2A_21-01965


title: COVIRS_90_V1_21-01960


title: COVIRS_58_V2A_21-01972


title: COVIRS_37_V2A_21-01964


title: COVIRS_91_V1_21-01961


title: COVIRS_89_V1_21-01959


title: COVIRS_87_V0_21-01975


title: COVIRS_36_V2A_21-01963


title: COVIRS_87_V1_21-01957


title: COVIRS_86_V1_21-01956


title: COVIRS_85_V0_21-01955


title: COVIRS_81_V0_21-01954


title: COVIRS_88_V1_21-01958


title: COVIRS_79_V0_21-01953


title: COVIRS_77_V0_21-01952


title: COVIRS_76_V0_21-01951


title: COVIRS_76_V2A_21-01949


title: COVIRS_74_V0_21-01950


title: COVIRS_73_V2A_21-01946


title: COVIRS_74_V2A_21-01947


title: COVIRS_35_V2A_21-01962


title: COVIRS_72_V2A_21-01945


title: COVIRS_70_V2A_21-01943


title: COVIRS_63_V2A_21-01938


title: COVIRS_64_V2A_21-01939


title: COVIRS_67_V2A_21-01941


title: COVIRS_74_V1_21-01932


title: COVIRS_79_V1_21-01935


title: COVIRS_81_V1_21-01936


title: COVIRS_66_V2A_21-01940


title: COVIRS_76_V1_21-01933


title: COVIRS_72_V0_21-01930


title: COVIRS_85_V1_21-01937


title: COVIRS_71_V0_21-01929


title: COVIRS_73_V0_21-01931


title: COVIRS_77_V1_21-01934


title: COVIRS_68_V0_21-01927


title: COVIRS_70_V0_21-01928


title: COVIRS_64_V0_21-01926


title: COVIRS_90_V2A_21-01925


title: COVIRS_89_V2A_21-01924


title: COVIRS_75_V2A_21-01948


title: COVIRS_88_V2A_21-01923


title: COVIRS_85_V2A_21-01920


title: COVIRS_86_V2A_21-01921


title: COVIRS_71_V2A_21-01944


title: COVIRS_68_V2A_21-01942


title: COVIRS_83_V2A_21-01918


title: COVIRS_81_V2A_21-01917


title: COVIRS_78_V2A_21-01915


title: COVIRS_79_V2A_21-01916


title: COVIRS_84_V2A_21-01919


title: COVIRS_77_V2A_21-01914


title: COVIRS_73_V1_21-01913


title: COVIRS_70_V1_21-01910


title: COVIRS_64_V1_21-01908


title: COVIRS_68_V1_21-01909


title: COVIRS_62_V0_21-01906


title: COVIRS_51_V0_21-01904


title: COVIRS_63_V0_21-01907


title: COVIRS_54_V0_21-01905


title: COVIRS_46_V0_21-01902


title: COVIRS_71_V1_21-01911


title: COVIRS_100_V2A_21-01898


title: COVIRS_103_V2A_21-01900


title: COVIRS_101_V2A_21-01899


title: COVIRS_104_V2A_21-01901


title: COVIRS_87_V2A_21-01922


title: COVIRS_97_V2A_21-01896


title: COVIRS_99_V2A_21-01897


title: COVIRS_96_V2A_21-01895


title: COVIRS_93_V2A_21-01892


title: COVIRS_94_V2A_21-01893


title: COVIRS_95_V2A_21-01894


title: COVIRS_92_V2A_21-01891


title: COVIRS_91_V2A_21-01890


title: COVIRS_63_V1_21-01889


title: COVIRS_72_V1_21-01912


title: COVIRS_62_V1_21-01888


title: COVIRS_51_V1_21-01886


title: COVIRS_49_V0_21-01903


title: COVIRS_46_V1_21-01884


title: COVIRS_49_V1_21-01885


title: COVIRS_37_V0_21-01882


title: COVIRS_35_V0_21-01881


title: COVIRS_25_V0_21-01880


title: COVIRS_38_V0_21-01883


title: COVIRS_7_V1_21-01742

value: Peripheral blood

value: ChAdOx1 nCoV-19


title: COVIRS_24_V0_21-01879


title: COVIRS_39_V1_21-01747


title: COVIRS_2_V0_21-01744


title: COVIRS_22_V0_21-01878


title: COVIRS_9_V1_21-01743


title: COVIRS_1_V0_21-01741


title: COVIRS_84_V0_21-01740


title: COVIRS_21_V1_21-01739


title: COVIRS_11_V1_21-01738


title: COVIRS_5_V0_21-01745


title: COVIRS_96_V0_21-01736


title: COVIRS_6_V1_21-01734


title: COVIRS_54_V1_21-01887


title: COVIRS_8_V1_21-01735


title: COVIRS_4_V0_21-01733


title: COVIRS_3_V0_21-01737


title: COVIRS_67_V0_21-01732


title: COVIRS_5_V1_21-01731


title: COVIRS_2_V1_21-01730


title: COVIRS_83_V0_21-01729


title: COVIRS_53_V0_21-01728


title: COVIRS_12_V1_21-01746


title: COVIRS_84_V1_21-01726


title: COVIRS_1_V1_21-01727


title: COVIRS_58_V0_21-01724


title: COVIRS_96_V1_21-01722


title: COVIRS_75_V0_21-01721


title: COVIRS_48_V0_21-01720


title: COVIRS_56_V0_21-01716


title: COVIRS_47_V0_21-01713


title: COVIRS_67_V1_21-01718


title: COVIRS_83_V1_21-01715


title: COVIRS_41_V0_21-01712


title: COVIRS_53_V1_21-01714


title: COVIRS_66_V1_21-01711


title: COVIRS_58_V1_21-01710


title: COVIRS_20_V0_21-01708


title: COVIRS_48_V1_21-01706


title: COVIRS_36_V0_21-01709


title: COVIRS_75_V1_21-01707


title: COVIRS_43_V0_21-01705


title: COVIRS_60_V1_21-01703


title: COVIRS_16_V0_21-01704


title: COVIRS_56_V1_21-01702


title: COVIRS_10_V0_21-01700


title: COVIRS_28_V0_21-01701


title: COVIRS_3_V1_21-01723


title: COVIRS_66_V0_21-01725


title: COVIRS_39_V0_21-01697


title: COVIRS_47_V1_21-01699


title: COVIRS_16_V1_21-01719


title: COVIRS_12_V0_21-01696


title: COVIRS_60_V0_21-01717


title: COVIRS_9_V0_21-01693


title: COVIRS_20_V1_21-01694


title: COVIRS_7_V0_21-01692


title: COVIRS_36_V1_21-01695


title: COVIRS_41_V1_21-01698


title: COVIRS_21_V0_21-01689


title: COVIRS_28_V1_21-01687


title: COVIRS_10_V1_21-01686


title: COVIRS_43_V1_21-01691


title: COVIRS_8_V0_21-01685


title: COVIRS_40_V1_21-01690


title: COVIRS_6_V0_21-01684


title: Human islet

status: Public on Sep 16 2022

city: Fujisawa

first: Hideyuki

last: Hiyoshi

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

data_processing:
Sequenced reads were aligned to the human GRCh38 reference and count UMIs using Cell Ranger v2.0.1 software.
Gene barcode matrices were generated from Cell Ranger software.
Assembly: GRCh38
Supplementary files format and content: Matrix table with UMI counts for every gene and every cell within sample; barcodes.tsv, genes.tsv, matrix.mtx.

source_name: pancreatic islet

extract_protocol: Single-cell RNA-seq libraries were generated using the 10x Genomics ChromiumTM controller and Chromium Single Cell 3' kits v2 (10x Genomics) according to the manufacturer’s instructions.

tag: cell origin

value: cadaveric human tissue

value: pancreatic islet


title: s6-iPIC-A_batch1

source_name: pancreatic endocrine like cells

value: induced pluripotent stem cells

value: pancreatic endocrine like cells


title: s6-iPIC-B


title: s6-iPIC-A_batch2


title: K562-3T3_K4_MulTI_seq_ICELL8_rep1_(20210122_MM_HsMm_1992-96K4)

status: Public on Sep 14 2022

city: Chapel Hill

first: Michael

last: Meers

state: NC

address: 250 Bell Tower Dr.

institute: UNC Chapel Hill

description: H3K4me2-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in a mixture of K562 and NIH3T3 cells, sequentially profiled, amplified on ICELL8

library_source: genomic

data_processing:
Genome_build: UCSC hg19, mm10
A. Bulk MulTI-Tag: 1. We used Bowtie2 2.4.2 with options --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700 to map the paired-end 25bp reads to a hybrid reference sequence of HG19 (Homo sapiens) and MM10 (Mus musculus) obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a fragment bed file <chr> <start> <stop>, then used bedtools genomecov 2.28.0 to generate a track in bigwig format. Each chromosome annotation is appended with the species of origin (e.g. chr1_hs or chr1_mm (Supplementary file bw).  B. iCell8 system: We used a custom python script to demultiplex and annotate fastq reads, then used custom software to analyse the single cell data. The custom software is available from https://github.com/mpmeers/MeersEtAl_MulTI-Tag.

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

source_name: MulTI-Tag

extract_protocol:
MulTI-Tag was carried out as follows: Nuclei were incubated with pATn5-i5 adapter-primary antibody conjugate complexes and tagmented sequentially, then secondary antibody-pATn5-i7 adapter complexes were bound and tagmented. Tagmented samples were resuspended in 10 mM TAPS with 0.1% SDS, incubated at 58 degrees C for 1 hour, then SDS was neutralized by adding a final concentration of 0.3% Triton X-100. Samples proceeded directly to amplification of tagmented DNA inserts with barcoded primers. See also PMID 32913232 .
MulTI-Tag was carried out using pA-Tn5-adapter-antibody conjugate complexes to integrate barcoded adapters via tagmentation directly to DNA for each antibody target on both sides of the insert, so that the DNA that is released is already a barcoded library.

tag: antibody

value: H3K4me2 Acite Motif 39679 Lot 31718013; cell type:K562 human immortalised myelogenous leukemia cell line, NIH3T3 mouse immortalized embryonic fibroblast cell line


title: s6-iPIC-A_static

tag: cell type


title: K562-3T3_K4_MulTI_indiv_ICELL8_rep1_(20210122_MM_HsMm_1990-94)

description: MulTI-Tag for H3K4me2 in a mixture of K562 and NIH3T3 cells, individually profiled, amplified on ICELL8


title: iPIC


title: K562-3T3_K36_MulTI_indiv_ICELL8_rep1_(20210122_MM_HsMm_1991-95)

description: MulTI-Tag for H3K36me3 in a mixture of K562 and NIH3T3 cells, individually profiled, amplified on ICELL8

value: H3K36me3 Active Motif 61021 Lot 23819012; cell type:K562 human immortalised myelogenous leukemia cell line, NIH3T3 mouse immortalized embryonic fibroblast cell line


title: K562-3T3_K36_MulTI_seq_ICELL8_rep1_(20210122_MM_HsMm_1992-96K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in a mixture of K562 and NIH3T3 cells , sequentially profiled, amplified on ICELL8


title: K562-3T3_K27_MulTI_seq_ICELL8_rep1_(20210122_MM_HsMm_1992-96K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in a mixture of K562 and NIH3T3 cells, sequentially profiled, amplified on ICELL8

value: H3K27me3 Cell Signaling Technology CST9733 Lot 16; cell type:K562 human immortalised myelogenous leukemia cell line, NIH3T3 mouse immortalized embryonic fibroblast cell line


title: H1_K4_MulTI_seq_(20210122_MM_Hs_MPM1960K4)

description: H3K4me2-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled

data_processing:
Genome_build: UCSC hg19
A. Bulk MulTI-Tag: 1. We used Bowtie2 2.4.2 with options --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700 to map the paired-end 25bp reads to HG19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a fragment bed file <chr> <start> <stop>, then used bedtools genomecov 2.28.0 to generate a track in bigwig format (Supplementary file). B. iCell8 system: We used a custom python script to demultiplex and annotate fastq reads, then used custom software to analyse the single cell data. The custom software is available from https://github.com/mpmeers/MeersEtAl_MulTI-Tag.

value: H3K4me2 Acite Motif 39679 Lot 31718013; cell type:H1 hESC, human embryonic stem cells


title: H1_K36_MulTI_seq_(20210122_MM_Hs_MPM1960K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled

value: H3K36me3 Active Motif 61021 Lot 23819012; cell type:H1 hESC, human embryonic stem cells


title: H1_K4_MulTI_indiv_(20210122_MM_Hs_MPM1958)

description: MulTI-Tag for H3K4me2 in H1 cells, individually profiled


title: H1_K36_MulTI_seq_ICELL8_(20210524_MM_Hs_MPM2246K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: COVIRS_11_V0_21-01688

value: Female


title: K562-3T3_K27_MulTI_indiv_ICELL8_rep1_(20210122_MM_HsMm_1989-93)

description: MulTI-Tag for H3K27me3 in a mixture of K562 and NIH3T3 cells, individually profiled, amplified on ICELL8


title: H1_K36_MulTI_indiv_(20210122_MM_Hs_MPM1959)

description: MulTI-Tag for H3K36me3 in H1 cells, individually profiled


title: H1_K27_MulTI_seq_ICELL8_(20210524_MM_Hs_MPM2246K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8

value: H3K27me3 Cell Signaling Technology CST9733 Lot 16; cell type:H1 hESC, human embryonic stem cells


title: K562_Ser5_MulTI_secondary_indiv_(20190716_MM_Hs_MPM1072)

description: Secondary antibody conjugate MulTI-Tag for PolIIS5P in K562 cells, individually profiled

value: PolIIS5P Abcam ab5408 Lot GR3264297-2; cell type:K562 human immortalised myelogenous leukemia cell line


title: K562_Ser5_MulTI_primary_seq_rep2_(20200610_MM_Hs_MPM1531Ser5)

description: PolIIS5P-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: K562_Ser5_MulTI_secondary_seq_(20190716_MM_Hs_MPM1075Ser5)

description: PolIIS5P-barcoded data from secondary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: H1_K27_MulTI_indiv_(20210122_MM_Hs_MPM1957)

description: MulTI-Tag for H3K27me3 in H1 cells, individually profiled


title: K562_Ser5_MulTI_secondary_comb_(20190716_MM_Hs_MPM1076Ser5)

description: PolIIS5P-barcoded data from secondary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: K562_Ser5_MulTI_primary_seq_rep1_(20200511_MM_Hs_MPM1489Ser5)


title: K562_Ser5_MulTI_primary_indiv_rep1_(20200511_MM_Hs_MPM1488)

description: Primary antibody conjugate MulTI-Tag for PolIIS5P in K562 cells, individually profiled


title: K562_Ser5_MulTI_primary_indiv_rep2_(20200610_MM_Hs_MPM1528)


title: K562_K4_MulTI_seq_ICELL8_(20210524_MM_Hs_MPM2244K4)

description: H3K4me2-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8

value: H3K4me2 Acite Motif 39679 Lot 31718013; cell type:K562 human immortalised myelogenous leukemia cell line


title: K562_Ser5_MulTI_primary_comb_(20200511_MM_Hs_MPM1490Ser5)

description: PolIIS5P-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: K562_K4_MulTI_seq_(20210122_MM_Hs_MPM1956K4)

description: H3K4me2-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled


title: K562_K4_MulTI_seq_ICELL8_rep1_(20210122_MM_Hs_MPM1964K4)


title: H1_K4_MulTI_seq_ICELL8_(20210524_MM_Hs_MPM2246K4)

description: H3K4me2-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: K562_K4_MulTI_indiv_(20210122_MM_Hs_MPM1954)

description: MulTI-Tag for H3K4me2 in K562 cells, individually profiled


title: K562_K4_MulTI_seq_ICELL8_rep2_(20210315_MM_Hs_MPM2060K4)


title: K562_K4_MulTI_indiv_ICELL8_rep1_(20210122_MM_Hs_MPM1962)

description: MulTI-Tag for H3K4me2 in K562 cells, individually profiled, amplified on ICELL8


title: K562_K36_MulTI_seq_ICELL8_(20210524_MM_Hs_MPM2244K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8

value: H3K36me3 Active Motif 61021 Lot 23819012; cell type:K562 human immortalised myelogenous leukemia cell line


title: K562_K36_MulTI_seq_ICELL8_rep2_(20210315_MM_Hs_MPM2060K36)


title: K562_K4_MulTI_indiv_ICELL8_rep2_(20210315_MM_Hs_MPM2058)


title: K562_K36_MulTI_seq_ICELL8_rep1_(20210122_MM_Hs_MPM1964K36)


title: K562_K36_MulTI_seq_(20210122_MM_Hs_MPM1956K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled


title: H1_K27_MulTI_seq_(20210122_MM_Hs_MPM1960K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled


title: K562_K36_MulTI_indiv_(20210122_MM_Hs_MPM1955)

description: MulTI-Tag for H3K36me3 in K562 cells, individually profiled


title: K562_K27_MulTI_seq_ICELL8_(20210524_MM_Hs_MPM2244K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8

value: H3K27me3 Cell Signaling Technology CST9733 Lot 16; cell type:K562 human immortalised myelogenous leukemia cell line


title: K562_K36_MulTI_indiv_ICELL8_rep2_(20210315_MM_Hs_MPM2059)

description: MulTI-Tag for H3K36me3 in K562 cells, individually profiled, amplified on ICELL8


title: K562_K36_MulTI_indiv_ICELL8_rep1_(20210122_MM_Hs_MPM1963)


title: K562_K27_MulTI_seq_(20210122_MM_Hs_MPM1956K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled


title: K562_K27_MulTI_seq_ICELL8_rep2_(20210315_MM_Hs_MPM2060K27)


title: K562_K27_MulTI_secondary_seq_(20190716_MM_Hs_MPM1075K27)

description: H3K27me3-barcoded data from secconday antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: K562_K27_MulTI_secondary_comb_(20190716_MM_Hs_MPM1076K27)

description: H3K27me3-barcoded data from secconday antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: K562_K27_MulTI_primary_seq_rep2_(20200610_MM_Hs_MPM1531K27)

description: H3K27me3-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: K562_K27_MulTI_primary_indiv_rep1_(20200511_MM_Hs_MPM1487)

description: Primary antibody conjugate MulTI-Tag for H3K27me3 in K562 cells, individually profiled


title: K562_K27_MulTI_primary_indiv_rep2_(20200610_MM_Hs_MPM1527)


title: K562_K27_MulTI_primary_comb_(20200511_MM_Hs_MPM1490K27)

description: H3K27me3-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: K562_K27_MulTI_indiv_(20210122_MM_Hs_MPM1953)

description: MulTI-Tag for H3K27me3 in K562 cells, individually profiled


title: K562_Ser5_CUTnTag_indiv_(20190716_MM_Hs_MPM1070)

description: CUT&Tag for PolIIS5P in K562 cells, individually profiled

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from the alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19_fragments.bed.gz).  3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (137567484) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: CUT&Tag

extract_protocol: CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: K562_K27_MulTI_indiv_ICELL8_rep1_(20210122_MM_Hs_MPM1961)

description: MulTI-Tag for H3K27me3 in K562 cells, individually profiled, amplified on ICELL8


title: K562_Ser5_CUTnTag_comb_(20190716_MM_Hs_MPM1074Ser5)

description: PolIIS5P-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: ADJ5, scRNAseq

status: Public on Sep 13 2022

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

country: China

institute: Peking University First Hospital

description: 10x Genomics

data_processing:
Raw data (BCL files) from Illumina Novaseq6000 platform was converted to fastq files using Illumina-implemented software bcl2fastq (v2.19.0.316). cDNA reads were aligned to human reference genome (GRCh38). Low-quality cells and genes filtering, barcode and UMI counting were performed with the cellranger software (v6.1.2) to obtain the filtered gene-cell matrixes. Next, gene-cell matrixes were imported into R software to further filtered out low-quality cells (< 500 genes/cell, > 25% mitochondria genes, < 1000 transcripts/cell) and genes (<10 cells/gene) using ‘Seurat’ R package (v3.2.3). Gene expression levels were normalized (LogNormalize) with “NormalizedData” function. A total of 2,000 highly variable genes were selected and used to conduct PCA reduction dimension. The t-distributed stochastic neighbor embedding (t-SNE) was performed. The ‘Soupx’ R package was applied to reduce the ambient mRNA contamination. Doublets were identified using the ‘DoubletFinder’ R package (v2.0.3), assuming that it was around 5% doublet formation rate to the loaded cells per specimen in a droplet channel. In addition, the ‘Harmony’ R package (https://github.com/immunogenomics/harmony) was used to integrate gene-cell matrixes derived from different specimens. We identified each cell cluster by matching the cluster-specific genes with known signatures of cell populations reported in previous studies and CellMarker database.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Adjacent noncancerous pancreatic tissue

extract_protocol:
All fresh resection specimens were preserved in the tissue storage solution (Miltenyi, Cat. no. 130-100-008) on ice and transported to the laboratory in CapitalBio Technology company within 1.5-2 hours. To ensure the success of tissue dissociation, multiple resection specimens from the same patients were digested. All specimens were cut into around 1 mm pieces and incubated in an optimal digestive solution, including enzyme cocktail, consisting of the Type VIII Collagenase (Sigma-Aldrich, Cat. no. C2139), DNase I (Sigma-Aldrich, Cat. no. D5025), trypsin inhibitor (Sigma-Aldrich, Cat. no. T6522), and Dispase II (neutral protease, grade II, Sigma-Aldrich, Cat. no. 4942078001). The single cell suspension was filtered with a 40 μm cell strainer (BD, Cat. no. 352340), then incubated with red blood cell lysis buffer (Roche, Cat. no. 11814389001) at 4°C for 10 minutes.
The concentration of single cell suspension was determined using the Count Star instrument and adjusted to 1000 cells/μl. The cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion using single cell 3’ Library and Gel Bead Kit v3.1 (10x Genomics, Cat. No. 1000121) and Chromium Next GEM Chip G Single Cell Kit (10x Genomics, Cat. No. 1000120) according to the manufacturer’s instructions. Briefly, cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were loaded to each channel, and the target cell will be captured about 3000 cells per channel. Captured cells were lysed and the released RNA were barcoded by reverse transcription in each GEM. Reverse transcription was completed in 200 ul tubes (NEST Biotechnology, Cat. No. 401001) on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 minutes, then at 85°C for 5 min, and hold at 4°C. The cDNA libraries were generated, amplified, and quality assessed using the Agilent 4200. Finally, the cDNA libraries were sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with paired-end 150 bp (PE150) reading strategy.

value: Adjacent noncancerous pancreatic tissue

value: No treatment


title: K562_K27_MulTI_indiv_ICELL8_rep2_(20210315_MM_Hs_MPM2057)


title: K562_K27_CUTnTag_indiv_(20190716_MM_Hs_MPM1069)

description: CUT&Tag for H3K27me3 in K562 cells, individually profiled


title: ADJ4, scRNAseq

description: 10x Genomics


title: K562_K27_CUTnTag_seq_(20190716_MM_Hs_MPM1073K27)

description: H3K27me3-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: K562_K27_CUTnTag_comb_(20190716_MM_Hs_MPM1074K27)

description: H3K27me3-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: MES5_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2619K4m1)

status: Public on Jul 17 2022

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 5 cells, sequentially profiled, amplified on ICELL8

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map  paired-end reads to the reference sequence (Homo sapiens UCSC hg19 reference genome build).  2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments.  3. We used bedtools genomecov to make a count bedgraph file. 4. We used Kent_tools bedGraphToBigWig to convert the bedgraph files to bigwig files (Supplementary .bw).

value: Day 5 differentiated mesoderm cells


title: MES4_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2618K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 4 cells, sequentially profiled, amplified on ICELL8

value: H3K36me3 Active Motif 61021 Lot 23819012

value: Day 4 differentiated mesoderm cells


title: MES5_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2619K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 5 cells, sequentially profiled, amplified on ICELL8

value: H3K27me3 Cell Signaling Technology CST9733 Lot 16


title: ADJ3, scRNAseq

description: 10x Genomics


title: MES4_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2618K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 4 cells, sequentially profiled, amplified on ICELL8


title: 22RV1_IgG

status: Public on Aug 29 2022

city: Nanjing

first: jun

last: wang

state: Jiangsu

address: No. 163 Xianlin Avenue, Qixia District

department: IMB

institute: Nanjing University

data_processing:
Fastq files were mapped to the reference genome (hg19) using bowtie2.3.5.
The non-primary alignment, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of CUT&RUN signals.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: 22Rv1 cells

growth_protocol: 22Rv1 cells, either the parental cells or those with the stably expressed HA-tagged EZH2 (carrying WT TAD domain or the TAD-transactivation-dead mutant (FA), were grown in the RPMI1640 base medium plus 10% FBS and 1% antibiotics. For EZH2 and H3K27me3 CUT&RUN, IgG was used as negative control; and for anti-HA CUT&RUN, 22Rv1 cells with empty vector (EV) were used as negative control. For compound treatment, cells were treated for 24 hours with either DMSO (control) or 2.5 µM of MS177.

extract_protocol:
DNA purification was carried out with the PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, #T1030).
Libraries were prepared by NEBNext Ultra II kit (NEB, #E7645L)

treatment_protocol: 1 million of cells was collected, washed and bound to ConA beads. Cell:bead sample was incubated with the indicated antibodies overnight and then washed and treated with pAG-MNase, followed by adding 2mM CaCl2 to activate pAG-MNase. Solubilized chromatin was then released using the CUT&RUN stop buffer.

value: 22Rv1 cells

tag: antibody used

value: Rabbit anti-IgG (CST 2729)


title: MES5_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2619K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 5 cells, sequentially profiled, amplified on ICELL8


title: hESC_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2611K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in hESCs, sequentially profiled, amplified on ICELL8

value: H1 hESC, human embryonic stem cells


title: K562_K27_MulTI_seq_ICELL8_rep1_(20210122_MM_Hs_MPM1964K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8


title: K562_K27_MulTI_secondary_indiv_(20190716_MM_Hs_MPM1071)

description: Secondary antibody conjugate MulTI-Tag for H3K27me3 in K562 cells, individually profiled


title: MES3_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2617K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 3 cells, sequentially profiled, amplified on ICELL8

value: Day 3 differentiated mesoderm cells


title: MES4_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2618K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 4 cells, sequentially profiled, amplified on ICELL8


title: MES2_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2616K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 2 cells, sequentially profiled, amplified on ICELL8

value: Day 2 differentiated mesoderm cells


title: MES2_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2616K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 2 cells, sequentially profiled, amplified on ICELL8


title: K562_K27_MulTI_primary_seq_rep1_(20200511_MM_Hs_MPM1489K27)

description: H3K27me3-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: MES3_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2617K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 3 cells, sequentially profiled, amplified on ICELL8


title: MES2_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2616K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 2 cells, sequentially profiled, amplified on ICELL8


title: hESC_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2611K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in hESCs, sequentially profiled, amplified on ICELL8


title: hESC_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2611K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in hESCs, sequentially profiled, amplified on ICELL8


title: K562_K27_MulTI_seq_ICELL8_5_(220301_MM_Hs_MPM2587K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K4me1 in K562 cells, sequentially profiled, amplified on ICELL8

value: K562 human immortalised myelogenous leukemia cell line


title: K562_K27_MulTI_seq_ICELL8_4_(220301_MM_Hs_MPM2584K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K9me3 in K562 cells, sequentially profiled, amplified on ICELL8


title: K562_K4m1_MulTI_seq_ICELL8_5_(220301_MM_Hs_MPM2587K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3 and H3K4me1 in K562 cells, sequentially profiled, amplified on ICELL8


title: K562_K27_MulTI_seq_ICELL8_6_(220301_MM_Hs_MPM2590K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8


title: K562_Ser5_CUTnTag_seq_(20190716_MM_Hs_MPM1073Ser5)

description: PolIIS5P-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: K562_Ser5_MulTI_seq_ICELL8_3_(220301_MM_Hs_MPM2581Ser5)

description: PolIIS5P-barcoded data from MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled, amplified on ICELL8

value: PolIIS5P Abcam ab5408 Lot GR3264297-2


title: K562_K36_MulTI_seq_ICELL8_6_(220301_MM_Hs_MPM2590K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8


title: K562-H1_K27_MulTI_seq_ICELL8_4_(220301_MM_Hs_MPM2586K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K9me3 in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8

value: K562 human immortalised myelogenous leukemia cell line; H1 hESC, human embryonic stem cells


title: H1_Ser5_MulTI_seq_ICELL8_3_(220301_MM_Hs_MPM2582Ser5)

description: PolIIS5P-barcoded data from MulTI-Tag for H3K27me3 and PolIIS5P in H1 cells, sequentially profiled, amplified on ICELL8


title: K562-H1_K9_MulTI_seq_ICELL8_4_(220301_MM_Hs_MPM2586K9)

description: H3K9me3-barcoded data from MulTI-Tag for H3K27me3 and H3K9me3 in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8

value: H3K9me3 Abcam ab8898 Lot GR3302452-1


title: K562-3T3_K36_MulTI_seq_ICELL8_(220120_MM_HsMm_MPM2547K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in a mixture of K562 and 3T3 cells, sequentially profiled, amplified on ICELL8

value: K562 human immortalised myelogenous leukemia cell line; NIH3T3 mouse immortalised fibroblast cell line


title: H1_K4m1_MulTI_seq_ICELL8_5_(220301_MM_Hs_MPM2588K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3 and H3K4me1 in H1 cells, sequentially profiled, amplified on ICELL8


title: K562_K27_MulTI_seq_ICELL8_3_(220301_MM_Hs_MPM2581K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled, amplified on ICELL8


title: K562-H1_K4m1_MulTI_seq_ICELL8_5_(220301_MM_Hs_MPM2589K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3 and H3K4me1 in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8


title: K562-H1_K27_MulTI_seq_ICELL8_6_(220301_MM_Hs_MPM2592K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8


title: MES3_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2617K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in MES Day 3 cells, sequentially profiled, amplified on ICELL8


title: K562_K9_MulTI_seq_ICELL8_4_(220301_MM_Hs_MPM2584K9)

description: H3K9me3-barcoded data from MulTI-Tag for H3K27me3 and H3K9me3 in K562 cells, sequentially profiled, amplified on ICELL8


title: K562-H1_K36_MulTI_seq_ICELL8_6_(220301_MM_Hs_MPM2592K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K9_MulTI_seq_ICELL8_4_(220301_MM_Hs_MPM2585K9)

description: H3K9me3-barcoded data from MulTI-Tag for H3K27me3 and H3K9me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: K562-3T3_K27_MulTI_indiv_ICELL8_(220120_MM_HsMm_MPM2545)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 in a mixture of K562 and 3T3 cells, amplified on ICELL8


title: K562-H1_K27_MulTI_seq_ICELL8_5_(220301_MM_Hs_MPM2589K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K4me1 in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8


title: K562-3T3_K36_MulTI_indiv_ICELL8_(220120_MM_HsMm_MPM2546)

description: H3K36me3-barcoded data from MulTI-Tag for H3K36me3 in a mixture of K562 and 3T3 cells, amplified on ICELL8


title: K562-H1_K27_MulTI_seq_ICELL8_3_(220301_MM_Hs_MPM2583K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and PolIIS5P in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8


title: K562-3T3_K27_MulTI_seq_ICELL8_(220120_MM_HsMm_MPM2547K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in a mixture of K562 and 3T3 cells, sequentially profiled, amplified on ICELL8


title: K562-H1_Ser5_MulTI_seq_ICELL8_3_(220301_MM_Hs_MPM2583Ser5)

description: PolIIS5P-barcoded data from MulTI-Tag for H3K27me3 and PolIIS5P in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K36_MulTI_seq_ICELL8_6_(220301_MM_Hs_MPM2591K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: ECT7_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2625K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 7 cells, sequentially profiled, amplified on ICELL8

value: Day 7 differentiated ectoderm cells


title: H1_K27_MulTI_seq_ICELL8_5_(220301_MM_Hs_MPM2588K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K4me1 in H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K27_MulTI_seq_ICELL8_6_(220301_MM_Hs_MPM2591K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K27_MulTI_seq_ICELL8_4_(220301_MM_Hs_MPM2585K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K9me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: ECT5_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2623K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 5 cells, sequentially profiled, amplified on ICELL8

value: Day 5 differentiated ectoderm cells


title: ECT4_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2622K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 4 cells, sequentially profiled, amplified on ICELL8

value: Day 4 differentiated ectoderm cells


title: H1_K27_MulTI_seq_ICELL8_3_(220301_MM_Hs_MPM2582K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and PolIIS5P in H1 cells, sequentially profiled, amplified on ICELL8


title: ECT5_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2623K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 5 cells, sequentially profiled, amplified on ICELL8


title: ECT7_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2625K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 7 cells, sequentially profiled, amplified on ICELL8


title: K562_Ser5_MulTI_primary_seq_rep2_(200610_MM_Hs_MPM1531Ser5)

description: PolIIS5P-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: ECT3_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2621K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 3 cells, sequentially profiled, amplified on ICELL8

value: Day 3 differentiated ectoderm cells


title: ECT3_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2621K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 3 cells, sequentially profiled, amplified on ICELL8


title: ECT7_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2625K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 7 cells, sequentially profiled, amplified on ICELL8

value: H3K36me3 Active Motif 61021 Lot 23819012


title: ECT6_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2624K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 6 cells, sequentially profiled, amplified on ICELL8

value: Day 6 differentiated ectoderm cells


title: ECT2_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2620K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 2 cells, sequentially profiled, amplified on ICELL8

value: Day 2 differentiated ectoderm cells


title: ECT6_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2624K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 6 cells, sequentially profiled, amplified on ICELL8


title: ECT6_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2624K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 6 cells, sequentially profiled, amplified on ICELL8

value: H3K27me3 Cell Signaling Technology CST9733 Lot 16


title: ECT5_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2623K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 5 cells, sequentially profiled, amplified on ICELL8


title: ECT2_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2620K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 2 cells, sequentially profiled, amplified on ICELL8


title: K562_Ser5_MulTI_secondary_seq_(190716_MM_Hs_MPM1075Ser5)

description: PolIIS5P-barcoded data from secondary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (hg19). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments.  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position. 4. We used Kent_tools bedGraphToBigWig to convert the bedgraph file to bigwig format (Supplementary file .bw).


title: ECT4_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2622K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 4 cells, sequentially profiled, amplified on ICELL8


title: K562_Ser5_MulTI_secondary_comb_(190716_MM_Hs_MPM1076Ser5)

description: PolIIS5P-barcoded data from secondary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: ECT3_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2621K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 3 cells, sequentially profiled, amplified on ICELL8


title: ECT4_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2622K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 4 cells, sequentially profiled, amplified on ICELL8


title: K562_Ser5_MulTI_primary_indiv_rep2_(200610_MM_Hs_MPM1528)

description: Primary antibody conjugate MulTI-Tag for PolIIS5P in K562 cells, individually profiled


title: K562_Ser5_MulTI_primary_seq_rep1_(200511_MM_Hs_MPM1489Ser5)


title: K562_Ser5_MulTI_primary_comb_(200511_MM_Hs_MPM1490Ser5)

description: PolIIS5P-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: K562_Ser5_MulTI_primary_indiv_rep1_(200511_MM_Hs_MPM1488)


title: K562_K4_MulTI_seq_ICELL8_(210524_MM_Hs_MPM2244K4)

description: H3K4me2-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8

value: H3K4me2 Acite Motif 39679 Lot 31718013


title: K562_Ser5_CUTnTag_seq_(190716_MM_Hs_MPM1073Ser5)

description: PolIIS5P-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: K562_K36_MulTI_seq_ICELL8_2_(211005_MM_Hs_MPM2350K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8


title: DE5_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2615K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 5 cells, sequentially profiled, amplified on ICELL8

value: Day 5 differentiated endoderm cells


title: K562_K27_MulTI_seq_ICELL8_2_(211005_MM_Hs_MPM2350K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8


title: DE4_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2614K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 4 cells, sequentially profiled, amplified on ICELL8

value: Day 4 differentiated endoderm cells


title: K562_Ser5_MulTI_secondary_indiv_(190716_MM_Hs_MPM1072)

description: Secondary antibody conjugate MulTI-Tag for PolIIS5P in K562 cells, individually profiled


title: K562_K27_MulTI_secondary_seq_(190716_MM_Hs_MPM1075K27)

description: H3K27me3-barcoded data from secconday antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: DE3_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2613K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 3 cells, sequentially profiled, amplified on ICELL8

value: Day 3 differentiated endoderm cells


title: K562_K36_MulTI_seq_ICELL8_(210524_MM_Hs_MPM2244K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8

value: K562 human immortalised myelogenous leukemia cell line


title: DE5_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2615K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 5 cells, sequentially profiled, amplified on ICELL8


title: K562_Ser5_CUTnTag_comb_(190716_MM_Hs_MPM1074Ser5)

description: PolIIS5P-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled

value: PolIIS5P Abcam ab5408 Lot GR3264297-2


title: DE5_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2615K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 5 cells, sequentially profiled, amplified on ICELL8


title: DE4_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2614K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 4 cells, sequentially profiled, amplified on ICELL8


title: ECT2_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2620K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in ECT Day 2 cells, sequentially profiled, amplified on ICELL8


title: DE4_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2614K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 4 cells, sequentially profiled, amplified on ICELL8


title: DE3_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2613K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 3 cells, sequentially profiled, amplified on ICELL8


title: K562_K27_MulTI_secondary_comb_(190716_MM_Hs_MPM1076K27)

description: H3K27me3-barcoded data from secconday antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: K562_K27_MulTI_primary_seq_rep2_(200610_MM_Hs_MPM1531K27)

description: H3K27me3-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: K562_K27_MulTI_primary_indiv_rep2_(200610_MM_Hs_MPM1527)

description: Primary antibody conjugate MulTI-Tag for H3K27me3 in K562 cells, individually profiled


title: DE2_K36_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2612K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 2 cells, sequentially profiled, amplified on ICELL8

value: Day 2 differentiated endoderm cells


title: DE2_K27_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2612K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 2 cells, sequentially profiled, amplified on ICELL8


title: K562_Ser5_CUTnTag_indiv_(190716_MM_Hs_MPM1070)

description: CUT&Tag for PolIIS5P in K562 cells, individually profiled


title: K562_K27_MulTI_secondary_indiv_(190716_MM_Hs_MPM1071)

description: Secondary antibody conjugate MulTI-Tag for H3K27me3 in K562 cells, individually profiled


title: DE3_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2613K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 3 cells, sequentially profiled, amplified on ICELL8


title: K562_K27_MulTI_primary_indiv_rep1_(200511_MM_Hs_MPM1487)


title: K562_K27_MulTI_seq_ICELL8_(210524_MM_Hs_MPM2244K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in K562 cells, sequentially profiled, amplified on ICELL8


title: K562_K27_CUTnTag_comb_(190716_MM_Hs_MPM1074K27)

description: H3K27me3-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: K562_K27_MulTI_primary_seq_rep1_(200511_MM_Hs_MPM1489K27)


title: K562_K27_MulTI_primary_comb_(200511_MM_Hs_MPM1490K27)

description: H3K27me3-barcoded data from primary antibody conjugate MulTI-Tag for H3K27me3 and PolIIS5P in K562 cells, simultaneously profiled


title: K562_K27_CUTnTag_indiv_(190716_MM_Hs_MPM1069)

description: CUT&Tag for H3K27me3 in K562 cells, individually profiled


title: DE2_K4m1_MulTI_seq_ICELL8_(220329_MM_Hs_MPM2612K4m1)

description: H3K4me1-barcoded data from MulTI-Tag for H3K27me3, H3K4me1, and H3K36me3 in DE Day 2 cells, sequentially profiled, amplified on ICELL8


title: K562_K27_CUTnTag_seq_(190716_MM_Hs_MPM1073K27)

description: H3K27me3-barcoded data from CUT&Tag for H3K27me3 and PolIIS5P in K562 cells, sequentially profiled


title: K562-H1_K36_MulTI_seq_ICELL8_2_(211005_MM_Hs_MPM2352K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8

value: K562 human immortalised myelogenous leukemia cell line; H1 hESC, human embryonic stem cells


title: K562-H1_K27_MulTI_seq_ICELL8_2_(211005_MM_Hs_MPM2352K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in a mixture of K562 and H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K4_MulTI_indiv_(210122_MM_Hs_MPM1958)

description: MulTI-Tag for H3K4me2 in H1 cells, individually profiled

value: H1 hESC, human embryonic stem cells


title: H1_K4_MulTI_seq_(210122_MM_Hs_MPM1960K4)

description: H3K4me2-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled


title: H1_K36_MulTI_seq_ICELL8_2_(211005_MM_Hs_MPM2351K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K27_MulTI_seq_ICELL8_2_(211005_MM_Hs_MPM2351K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3 and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K36_MulTI_indiv_(210122_MM_Hs_MPM1959)

description: MulTI-Tag for H3K36me3 in H1 cells, individually profiled


title: H1_K36_MulTI_seq_(210122_MM_Hs_MPM1960K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled


title: H1_K36_MulTI_seq_ICELL8_(210524_MM_Hs_MPM2246K36)

description: H3K36me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K27_MulTI_seq_ICELL8_(210524_MM_Hs_MPM2246K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: H1_K27_MulTI_seq_(210122_MM_Hs_MPM1960K27)

description: H3K27me3-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled


title: H1_K27_MulTI_indiv_(210122_MM_Hs_MPM1957)

description: MulTI-Tag for H3K27me3 in H1 cells, individually profiled


title: Surveillance biopsies [3MonthsSampleT27F2]

status: Public on Dec 23 2021

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

data_processing:
The sequencing data is pre-processed using the 10X Genomics software Cell Ranger. Downstream analysis is performed with the Seurat3 R package (Satija Lab). Combined analysis of the single-cell datasets generated from the different sample sources (LD and Surveillance biopsies) using Seurat (v3) included the following steps: filtering out of cells with <500 genes or >50% mitochondrial content default normalization, scaling based on sample mRNA count and mitochondrial RNA content, dimensionality reduction PCA (Principal component analysis) and UMAP (Uniform Manifold Approximation and Projection), sample integration using Harmony algorithm, standard unsupervised clustering, and the discovery of differentially expressed cell type-specific markers.
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix files in tab delimited format

source_name: Kidney biopsy

extract_protocol:
We leveraged the surveillance biopsy program at the University of Michigan, where biopsies are performed at time 0, 3-,6- and 12 months. For this study the time 0 biopsies from healthy living donors (controls) were obtained at the back table prior to perfusion. While surveillance biopsies were performed at 3- and 12 months.. As part of our established Human Kidney Transplant Transcriptomic Atlas (HKTTA) workflow Along with standard of care biopsy cores, patients consent for a single research core obtained with a 16-gauge needle. The research core was collected following a standardized protocol.12,13 The research core is then cut into three pieces (1-2 mg each) with Piece#1 stored in RNA laterTM solution for bulk transcriptome analysis, Piece #2 and Piece #3 put into in Cryostor CS10 Freeze Media solution (Biolife Solutions) for scRNA-seq analysis, and for future use including single nuclear studies respectively.  All clinical and research activities being reported are consistent with the Principles of the Declaration of Istanbul.
The generation of single-cell preparations was accomplished by enzymatic (Liberase TL) and mechanical dissociation for 12 minutes at 37˚C following our protocol previously published.12 Cells are filtered through a 50µm strainer, counted, and up to 10,000 viable cells are submitted to the Genomics Core facility for droplet-based high-throughput 10X GenomicsTM Chromium TM platform arrays. After droplet encapsulation, the 10X Genomics approach allows cell lysis, individual cell RNA molecular barcoding, and reverse transcription. Subsequently, cDNA libraries are generated and sequenced on an Illumina NovaSeq6000 platform as asymmetric paired-end runs (26X1paired-end generating more than 200 million raw sequence reads per sample

tag: time point

value: 3 months post transplantation biopsy

tag: biopsy

value: Surveillance biopsies


title: Surveillance biopsies [3MonthsSampleT2]


title: Surveillance biopsies [3MonthsSampleT98F2]


title: H1_K4_MulTI_seq_ICELL8_(210524_MM_Hs_MPM2246K4)

description: H3K4me2-barcoded data from MulTI-Tag for H3K27me3, H3K4me2, and H3K36me3 in H1 cells, sequentially profiled, amplified on ICELL8


title: Surveillance biopsies [3MonthsSampleT4]


title: Surveillance biopsies [3MonthsSampleT20]


title: Surveillance biopsies [3MonthsSampleT23]


title: Surveillance biopsies [12MonthsSampleT8F2]

value: 12 months post transplantation biopsy


title: Surveillance biopsies [12MonthsSampleT33F2]


title: Surveillance biopsies [12MonthsSampleT6]


title: Surveillance biopsies [12MonthsSampleT13]


title: Surveillance biopsies [12MonthsSampleT11F2]


title: Surveillance biopsies [12MonthsSampleT5F2]


title: Liver, R&Z_KO_3M_2

status: Public on Dec 10 2021

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description:
E11KOE
CountFile.csv

data_processing:
Basecalling by Illumina's standard pipeline
QC step, sickle reads with quality > Q20
QC step, trim_galore removing Illumina adaptors
Mapping step: STAR 2.5.0a extra paramaters outSAMmultNmax 1 --quantMode GeneCounts --outSAMunmapped Within
Quanitification step: featureCounts 1.5.0-p1 using NCBI mm10 gtf
Genome_build: mm10 (NCBI)
Supplementary_files_format_and_content: FeatureCounts output: Gene Name, Gene Length, Read Count

source_name: Liver

extract_protocol:
RNA was extracted from liver tissue using Quiagen Rneasy mini kit
SMARTSEQ2 protocol

value: adult liver

tag: genotype

value: Rnf43 and Znrf3 mutant

tag: chronic damage

value: No

tag: partial hepatectomy

value: 3 months

tag: strain


title: VPA adult-2

status: Public on May 01 2022

type: RNA

city: Kodaira

first: Satoshi

last: Watanabe

state: Tokyo

address: 4-1-1 Ogawa Higashi

institute: National Center of Neurology and Psychiatry

description: Gene expression data from VPA-exposed adult marmoset

hyb_protocol: The arrays were hybridized and washed using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were normalized by GCRMA.

label: biotin

organism: Callithrix jacchus

source_name: Cortical area 12 from VPA-exposed adult marmoset

label_protocol: Biotin-labeled cRNA was generated using the GeneChip 3'IVT Express Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: For production of VPA marmoset, pregnant marmoset was administered with VPA at post-conception days 60-66, and the offspring were used.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Marmosets were anesthesized with ketamine followed by pentobarbital. Diethylpyrocarbonate-treated phosphate-buffered saline was transcardially perfused. Cortical tissues were isolated and immersed in RNAlater (Thermo Fisher).

tag: animal id

tag: Sex

value: M

tag: treatment

value: VPA-exposed

tag: age (days)

tag: area

value: Area 12


title: Liver, R&Z_KO_3M_3

description:
E11KOF
CountFile.csv

tag: tissue


title: VPA adult-4

source_name: Cortical area TE from VPA-exposed adult marmoset

value: F

value: Area TE


title: VPA adult-6


title: UE adult-3

description: Gene expression data from unexposed adult marmoset

source_name: Cortical area TE from unexposed adult marmoset

value: unexposed (UE)


title: VPA adult-5


title: UE adult-6

source_name: Cortical area 12 from unexposed adult marmoset


title: UE adult-4


title: UE adult-5


title: UE adult-2


title: UE adult-1


title: Surveillance biopsies [3MonthsSampleT39]


title: VPA adult-1


title: VPA adult-3


title: LB4143T

status: Public on Oct 18 2021

city: Los Angeles

first: Willy

last: Hugo

state: California

address: 10833 Le Conte Ave

department: Medicine

institute: University of California, Los Angeles

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #41

data_processing:
The reads are first mapped to GRCh38 using cellranger software from 10x Genomics
Single-cell, gene-level raw read counts are read from cellranger output and analyzed using Seurat 4.0.0
The Seurat R object from the Seurat object after IntegrateData and ScaleData step across 40 samples are provided as processed data file
Subsequent clustering and pseudotime trajectory analyses are descibed in the full manuscript
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat R object of the integrated and scaled single cell data

source_name: GBM rec TIL

extract_protocol:
Dissociated CD45+ single cells were processed using Chromium Single Cell GEM, Library & Gel Bead Kit threough the Chromium controller from 10x Genomics.
The resulting single cell barcoded mRNA were reverse transcribed and cleaned as per 10x Genomic's protocol.
10x Genomics single cell RNA-Seq

value: no

value: 5' sequencing

tag: cell number


title: LB4117T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #39

source_name: GBM pembro TIL

value: yes


title: LB4112T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #38


title: LB4101T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #36


title: Surveillance biopsies [12MonthsSampleT12F2]


title: LB4130T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #40


title: LB4177T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #42


title: LB4102T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #37


title: LB4059T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #34

value: 3' sequencing


title: LB4038T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #33

source_name: GBM new TIL


title: LB4075T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #35


title: LB4180T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #43


title: LB4025T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #31


title: LB3667T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #29


title: LB3018T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #28


title: LB4015T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #26

data_processing:
The reads are first mapped to Grch38 using cellranger software from 10x Genomics
Single-cell, gene-level raw read counts are read from cellranger output and analyzed using Seurat
The normalized count and the metadata from the Seurat object after IntegrateData and ScaleData step across 27 samples are provided as processed data file
Subsequent clustering and pseudotime trajectory analyses are descibed in the full manuscript
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene level raw count matrix, barcode suffix is the sample number included in the 'description' field.

extract_protocol: Chromium Single Cell GEM, Library & Gel Bead Kit

value: GBM


title: LB3964T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #23


title: LB4003T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #24

source_name: GBM PD1 TIL


title: LB4024T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #27


title: LB4034T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #32


title: LB4006T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #25


title: LB3944T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #20


title: LB3914T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #15


title: LB3915T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #16


title: LB3941T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #19


title: LB3931T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #17


title: LB3963T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #22


title: LB3933T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #18


title: LB3865T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #10


title: LB3872T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #13


title: LB3853T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #7


title: LB3864T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #9


title: LB3836T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #6


title: LB3854T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #8


title: LB3771T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #3


title: LB3869T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #11


title: LB3851T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #30


title: LB3871T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #12


title: LB3612T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #2


title: LB3958T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #21


title: mK4 Zeb1 and Zeb2 DKO RNA-seq_rep3

status: Public on Jun 13 2021

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: RNA-seq on mK4 Zeb1 and Zeb2 DKO cells

data_processing:
Quality control using FastQC
Adapter sequences removed with Trim Galore
Mapped to mouse genome  version NCBI37/mm9
Read counts using featureCounts v1.6.2
Differential expression assessed using DESeq2 v1.26.0
Genome_build: Mouse genome version NCBI37/mm9
Supplementary_files_format_and_content: TPM expression matrix

source_name: mK4 cells

growth_protocol: mK4 cells grown in 10% FBS media and collected when reaching confluency

extract_protocol:
Invitrogen PureLink RNA Mini Kit
BGI in house mRNA library kit

tag: cell line

value: kidney metanephric mesenchyme cell line

tag: genotype/variation

value: mK4 Zeb1 and Zeb2 DKO


title: mK4 Zeb1 and Zeb2 DKO RNA-seq_rep2

description: RNA-seq on mK4 Zeb1 and Zeb2 DKO cells

tag: cell type


title: mK4 Zeb1 and Zeb2 DKO RNA-seq_rep1

description: RNA-seq on mK4 Zeb1 and Zeb2 DKO cells


title: mK4 Runx1KO Runx2-seq_rep2

status: Public on Jun 07 2021

description: Runx2 ChIP-seq in mK4 Runx1KO cells.

data_processing:
Quality control using FastQC.
Adapter sequences removed with Trim Galore.
Mapped to mouse genome version NCBI37/mm9.
Peaks called using MACS2.
Genome_build: Mouse genome version NCBI37/mm9/MGSCv37
Supplementary_files_format_and_content: bigWig, bed: Peak files.
Supplementary_files_format_and_content: mK4_TPM_matrix.txt: TPM expression matrix.

source_name: mK4 Runx1KO cells

growth_protocol: mK4 cells grown in 10% FBS media and collected when reaching confluency.

extract_protocol: Libraries following Illumina protocol.

tag: chip antibody

value: Runx2 Cell Signaling #8486


title: mK4 control Runx2 ChIP-seq_rep2

description: Runx2 ChIP-seq in mK4 WT cells.

value: WT


title: mK4 Runx1KO Runx2-seq_rep1

description: Runx2 ChIP-seq in mK4 Runx1KO cells.


title: mK4 control Runx2 ChIP-seq_rep1

description: Runx2 ChIP-seq in mK4 WT cells.


title: mK4 Runx1KO Runx2-seq_rep3

description: Runx2 ChIP-seq in mK4 Runx1KO cells.


title: mK4 Runx1KO ATAC-seq_rep3

description: ATAC-seq on mK4 Runx1KO cells.


title: mK4 control Runx1 ChIP-seq_rep3

description: Runx1 ChIP-seq in mK4 WT cells.

value: Runx1 Cell Signaling #8529


title: mK4 Runx1KO Runx1-seq_rep1

description: Runx1 ChIP-seq in mK4 Runx1KO cells.


title: mK4 Runx1KO ATAC-seq_rep2

description: ATAC-seq on mK4 Runx1KO cells.


title: mK4 control Runx1 ChIP-seq_rep1

description: Runx1 ChIP-seq in mK4 WT cells.


title: mK4 control ATAC-seq_rep2

description: ATAC-seq on mK4 WT cells.


title: mK4 Runx1KO Runx1-seq_rep3

description: Runx1 ChIP-seq in mK4 Runx1KO cells.


title: mK4 Runx1KO ATAC-seq_rep1

description: ATAC-seq on mK4 Runx1KO cells.


title: mK4 control Runx1 ChIP-seq_rep2

description: Runx1 ChIP-seq in mK4 WT cells.


title: mK4 control RNA-seq_rep3

description:
RNA-seq on mK4 WT cells.
Control-628-4_1
mK4_TPM_matrix.txt

extract_protocol: BGI in house mRNA library kit. RNA-seq polyA-tail amplified.


title: PLX4032-3

status: Public on May 22 2021

data_processing:
FASTQ files were mapped by HISAT2
Deduplicated BAMs are analyzed with htseq-count to get gene level raw counts
Genome_build: mm10
Supplementary_files_format_and_content: raw count file by htseq-count

source_name: Db/Db mouse diabetic model

extract_protocol:
RNA purification with RNeasy Mini from Qiagen (Cat # 74104)
KAPA RNA-Seq Library Preparation Kits
Poly A transcript enrichment, stranded, single end RNAseq

treatment_protocol: BRAFi: Vemurafenib 1uM

value: skin

value: treated with vemurafenib (PLX4032) for 16 days


title: mK4 Runx1KO RNA-seq_rep1

description:
RNA-seq on mK4 Runx1KO cells.
Runx1KO-499-7_1
mK4_TPM_matrix.txt


title: mK4 control RNA-seq_rep2

description:
RNA-seq on mK4 WT cells.
Control-468-8_1
mK4_TPM_matrix.txt


title: mK4 control ATAC-seq_rep1

description: ATAC-seq on mK4 WT cells.


title: LB3579T

description: 10x Genomics single cell barcoded mRNA from CD45+ fraction, Sample #1


title: DMSO-2

value: treated with vehicle for 16 days


title: PLX4032-1


title: mK4 control Runx2 ChIP-seq_rep3

description: Runx2 ChIP-seq in mK4 WT cells.


title: DMSO-3


title: PLX4032-2


title: mK4 control RNA-seq_rep1

description:
RNA-seq on mK4 WT cells.
Control-463-2_1
mK4_TPM_matrix.txt


title: DMSO-1


title: mK4 control ATAC-seq_rep3

description: ATAC-seq on mK4 WT cells.


title: mK4 Runx1KO RNA-seq_rep2

description:
RNA-seq on mK4 Runx1KO cells.
Runx1KO-502-2_1
mK4_TPM_matrix.txt


title: mK4 Runx1KO RNA-seq_rep3

description:
RNA-seq on mK4 Runx1KO cells.
Runx1KO-511-2_1
mK4_TPM_matrix.txt


title: CD14+.RNA.oxPAPC_7h.rep1

status: Public on May 14 2021

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

data_processing:
For GRO-Seq and RNA-Seq, reads have been trimmed to remove 3' A-stretches from the library preparation and for all libraries the low quality reads were excluded (minimum 97% of bp over quality cutoff 10).
GRO-Seq reads have been aligned to hg19 with bowtie allowing up to two mismatches and only one alignment per read.
RNA-Seq data have been mapped to hg19 using STAR v2.5.4b with ENCODE standard options for long RNA-seq pipeline.
microRNA-Seq data have been mapped to hg19 using STAR v2.5.4b with ENCODE standard options for small RNA-seq pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

source_name: human macrophages

growth_protocol: HUVECs and HAECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich); HASMC were cultrured in Medium 231 (Cascade Biologics®) supplemented with Smooth Muscle Growth Supplement (SMGS). CD14+/Macrophages were cultured in Medium RPMI 1640, supplemented with 10 % FBS, 100μg/ml streptomycin,100 U/ml penicillin, and 2 mM glutamine, 1 % Na-pyruvate, 1 % NEAA and supplemented with rHu M-CSF (50ng/ml; ThermoFisher Scientific).

extract_protocol:
Cells were treated for 10 min with cycloheximide (0,1mg/mL), washed with PBS and scraped into lysis buffer [1x Mammalian Polysome Buffer (Epicentre, Madison, Wisconsin), 1% Triton X-100, 1 mM DTT, 250 U/ml SUPERase Inhibitor, 7.1 U/ml Turbo DNase (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.A.) and 0.1 mg/ml Cycloheximide] on ice. To confirm the complete lysis of the cells, they were drawn up and expelled 4 times through a sterile 22-25 gauge needle. The cleared lysate was further treated with 10% SDS, snap-frozen in liquid nitrogen and stored at -80°C. Larger mRNAs (>200 nt) was purified with Zymo RNA Clean and Conc kit (Zymo Research, Irvine, California, U.S.A.) and rRNAs were eliminated using the Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA, U.S.A.). RNA was then fragmentated (RNA fragmentation reagent, Thermofisher) and dephosphorylated.
RNA fragments were poly-A tailed (PolyA polymerase, New England Biolabs, Ipswich, MA, USA) according to manufacturer's instructions, then, fragments were circularized and re-linearized.  The libraries were amplified by 11 to 16 cycles size selected (190–350 bp) and quantified (Qubit dsDNA HS Assay Kit on a Qubit fluorometer, Thermofisher, Carlsbad, CA, USA). Sequencing (single end 50 bases) with Illumina Hi-Seq2000 at EMBL GeneCore (Heidelberg, Germany).
GRO-seq: Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol-LS.
RNA-seq, miRNA-seq: One hour after collection of GRO-Seq samples (reflecting the lag in nascent transcription and mature RNAs), cells were treated for 10 min with cycloheximide (0,1mg/mL), washed with PBS and scraped into lysis buffer [1x Mammalian Polysome Buffer (Epicentre, Madison, Wisconsin), 1% Triton X-100, 1 mM DTT, 250 U/ml SUPERase Inhibitor, 7.1 U/ml Turbo DNase (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.A.) and 0.1 mg/ml Cycloheximide] on ice. To confim the complete lysis of the cells, they were drawn up and expelled 4 times through a sterile 22-25 gauge needle. The cleared lysate was further treated with 10% SDS, snap-frozen in liquid nitrogen and stored at -80°C. For RNA-Seq, larger mRNAs (>200 nt) was purified with Zymo RNA Clean and Conc kit (Zymo Research, Irvine, California, U.S.A.) and rRNAs were eliminated using the Ribo-Zero Gold rRNA Removal Kit (Illumina, San Diego, CA, U.S.A.). For miRNA-Seq, small RNA-fraction (17-200 bases) was obtained by adding ethanol to the flow through from Zymo RNA Clean and Conc kit and passing the RNA through a new column.
GRO-seq, RNA-seq: The RNA was fragmented (RNA fragmentation reagent, Thermofisher), dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). For GRO-Seq only immunopurification step was performed, where BrUTP-labeled run-on RNA was bound with anti-BrdUTP-coated agarose beads and precipitated overnight. FOr both GRO-Seq and RNA-Seq libraries, the RNA was polyadenylated, followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11-16 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: Hypoxia was achieved in Ruskinn Invivo2 400 hypoxia workstation (1% O2 and 5% CO2). OxPAPC has been generated from 1-palmitoyl-2-archidonoyl-sn-glycero-3-phophocholine [PAPC, 10 mg/ml (Avanti Polar Lipids, Inc)]. PAPC was exposed to air for 40h, then dissolved in chloroform and stored at -70 °C. At the start of the oxPAPC stimulation, chloroform was evaporated with nitrogen gas and lipids were re-suspended in growth medium to achieve a concentration of 30 μg/ml.

tag: timepoint

value: 7 hours

tag: stimulus

value: OxPAPC


title: CD14+.RNA.hypoxia_7h.rep1

value: Hypoxia


title: HASMC.RNA.hypo+oxP_7h.rep2

source_name: human aortic smooth muscle cells

value: Hypoxia+OxPAPC


title: CD14+.RNA.hypo+oxP_7h.rep2


title: CD14+.RNA.control.rep2

value: Control


title: CD14+.RNA.hypoxia_7h.rep2


title: HASMC.RNA.hypo+oxP_7h.rep1


title: HASMC.RNA.hypoxia_7h.rep2


title: HASMC.RNA.oxPAPC_7h.rep1


title: CD14+.RNA.hypo+oxP_7h.rep1


title: CD14+.RNA.oxPAPC_7h.rep2


title: HASMC.RNA.hypo+oxP_7h.rep3


title: HASMC.RNA.control.rep3


title: CD14+.RNA.control.rep1


title: HASMC.RNA.hypoxia_7h.rep3


title: HASMC.RNA.hypoxia_7h.rep1


title: HASMC.RNA.control.rep2


title: mK4 Runx1KO Runx1-seq_rep2

description: Runx1 ChIP-seq in mK4 Runx1KO cells.


title: HUVEC.RNA.hypo+oxP_7h.rep3

source_name: human umbilical vein endothelial cells


title: HUVEC.RNA.hypo+oxP_7h.rep1


title: HUVEC.RNA.hypo+oxP_7h.rep2


title: HASMC.RNA.control.rep1


title: HUVEC.RNA.hypoxia_7h.rep3


title: HASMC.RNA.oxPAPC_7h.rep2


title: HUVEC.RNA.hypoxia_7h.rep2


title: HASMC.RNA.oxPAPC_7h.rep3


title: HAEC.RNA.hypo+oxP_7h.rep3

source_name: primary human aortic endothelial cells


title: HAEC.RNA.hypo+oxP_7h.rep2


title: HAEC.RNA.hypoxia_7h.rep3


title: HAEC.RNA.hypoxia_7h.rep2


title: HAEC.RNA.hypoxia_7h.rep1


title: HAEC.RNA.hypo+oxP_7h.rep1