title: ED211124_b

description: lineage barcode RNA

data_processing:
Barcode dataset TrackerSeq: R2 FASTQ files were pre-processed using BBduk; the sequences to the left and right of the lineage barcodes were trimmed so that only the lineage barcode (BC) remained. Lineage barcodes shorter than 37 bp were discarded. Cell barcodes (Cell) were extracted from corresponding Seurat object of the dataset to generate a cell barcode whitelist. The extracted cell barcodes and UMIs were added to the read names of the lineage barcode FASTQ files. The resulting FASTQ files were processed by clonal_annotation.ipynb from LARRY (Klein lab), to output a sparse matrix in csv format, where rows were cells identified by individual cell barcodes and columns were lineage barcode, with 1 indicating its presence and 0 its absence. Only (Cell,UMI,BC) triples supported by at least 10 reads and (Cell,BC) pairs with at least 6 UMI were considered for further analyses. A CloneIDs were assigned to cell barcodes. The distance between the cell barcodes in the matrix could be determined by clustering the matrix using Jaccard similarity and average linkage, as demonstrated by Wagner et al. This could be accomplished by using the R function distance(method = ‘jaccard’) and hclust(method = ‘average’). The resulting dendrogram was cut at a height of 0.999 using cutree(hclust_avg, h = 0.999) to obtain the clonal groupings.
Csv files with columns for "CBC" and "Lineage-Barcode"
Assembly: mm10-2.1.0

source_name: Barcode dataset of ED211124


title: ED211111_b

status: Public on Feb 19 2024

type: SRA

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Neurobiology.

description:
lineage barcode RNA
Illumina NovaSeq 6000/ Illumina NextSeq 500

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

source_name: Barcode dataset of ED211111

extract_protocol:
embryonic tissue was collected in ice-cold Leibowitz medium  and papain dissociation was carried out (Wortington, #LK003150). Postnatal tissue was dissected in ice-cold bubbled ACSF and dissociatedwas carried out with the Miltenyi BioTech Neural Tissue Dissociation Kit (P) (#130-092-628)
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custom primers with standard Illumina adapters.

tag: tissue

value: Forebrain

tag: strain

tag: treatment

value: FACSorted for GFP

tag: age


title: Cerebellum, ChIP, replicate 4

city: LA JOLLA

first: Carlos

last: Guzman

state: CA

address: 9262 REGENTS RD

country: USA

institute: UCSD

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the mm10 genome using bowtie2 with the following parameters: “bowtie2 -q –very-sensitive-local -N 1”.
Peaks representing areas of strong polymerase binding were called using HOMER with the following parameters: “-style factor -fragLength 150”.
Bigwigs were created using HOMER's makeMultiWigHub.pl
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Cerebellum

growth_protocol: Female B6.Polr3a cKI/cKI mice were crossed to the appropriate Cre driver lines to generate Polr3a cKI/+, CreTg/+ mice. Tissue was harvested from 6-week-old mice

extract_protocol:
Extracted tissue was minced and then  fixed with 1% formaldehyde for 10 minutes. Crosslinking was terminated with 1/20th volume of 2.625M glycine. Samples were then washed with PBS containing protease inhibitors and lysed in ChIP RIPA buffer (50mM Tris-HCl, pH 7.5, 150mM NaCl, 1mM EDTA, 1% IPEGAL CA-630, 0.25% Na-Deoxycholate, 0.1% SDS, with cOmplete mini protease inhibitor cocktail (Roche)). The lysate was then sonicated using a Branson Digital Sonifier Probe (12-14x cycles, 40% amplitude, 10s ON, 30s OFF). Samples were centrifuged for 10 minutes at  4ºC. 1% of the lysate was saved as the DNA input control for the sample. For ChIP, 20 l Protein G Dynabeads and 2 g of FLAG antibody (Sigma F1804) were added to cleared lysate and rotated overnight at 4° C. Dynabeads were washed 3 times with Wash Buffer 1 (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), three times with Wash Buffer 3 (250 mM LiCl, 1 mM EDTA, 1% Triton X-100, 0.7% sodium deoxycholate), three times with TET (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.2% Tween 20), and resuspended in nuclease free water.
ChIP DNA from ChIP input and ChIP samples was used to prepare libraries using the NEBNext Ultra II Library preparation kit (NEB E7645S) and KAPA Single-Indexed Adapters for Illumina (Roche, KR1317) according to manufacturer’s protocol. Libraries were amplified by PCR for 14 cycles, size selected for 150-500bp fragments and sequenced, yielding ~10-40 million reads per sample.

value: Cerebellum

tag: chip antibody

value: FLAG (Sigma, F1804)

tag: genotype

value: Polr3a FLAG/FLAG


title: HGA114

type: RNA

city: Toronto

first: Cynthia

last: Hawkins

state: ON

address: 555 University Ave.

department: Pediatric Laboratory Medicine

country: Canada

institute: The Hospital for Sick Children

description: Sample 155

hyb_protocol: Per manufacturer protocols.

scan_protocol: Scanning was performed on the NanoString nCounter platform per the manufacturer protocols.

data_processing: All data analysis used Bioconductor version 3.14 or 3.16 packages in R version 4.1 or 4.2, respectively, unless otherwise stated. Raw NanoString data (RCC files) was processed using the NanoStringQCPro package (v1.26.0). For quality control, the geometric mean of the housekeeping genes was used as a metric of overall RNA quality and quantity, and samples with a value of < 100 were excluded. The data from all samples was normalized together using housekeeping genes and positive control genes as recommended in the NanoString data analysis guidelines. Briefly, for each sample a normalization was performed sequentially using first the positive controls and then the housekeeping genes. For each sample the geometric mean of the positive controls was calculated (geomeancontrol). The geometric mean of all the geometric means was then calculated (geomeangeomeans) and this was used to calculate a sample specific normalization factor (geomeangeomeans /geomeancontrol), which was multiplied by the gene counts for each sample. The same steps were then taken using the housekeeping genes instead of the positive controls, to provide the final normalized gene counts.

organism: Homo sapiens

source_name: pediatric brain tumor

label_protocol: Gene quantification was performed on the NanoString nCounter platform per the manufacturer protocols.

extract_protocol: Total RNA was extracted from FFPE and snap frozen tissue using RNAstorm FFPE and fresh frozen kits, respectively, as per the manufacturer's instructions (CellData). RNA concentration was measured (Nanodrop) and RNA integrity assessed using the Agilent 2100 bioanalyzer.

tag: tumor type

value: HGG

tag: nanostring cartridge


title: LPS-5_2

city: Hanover

first: Paula

middle: F.

last: Zamora

state: NH

address: 74 College st

institute: Geisel School of Medicine at Dartmouth

library_source: transcriptomic

data_processing:
Raw reads quality was first confirmed using FastQC v.0.11.9. Reads were trimmed for adapters and low-quality sequences using Trim Galore! v0.6.6 and aligned to the reference human genome GRCh38/hg38 using STAR v2.6.1d.
Assembly: Reads mapping to exons were assigned using featureCounts v2.0.1. Quality control was tracked using MultiQC v1.9.
Supplementary files format and content: Csv files, raw transcript counts for each treatment

source_name: Bronchial epithelium

growth_protocol: CFBE41o- cells were cultured in Minimal Essential Media supplemented with 10% of heat-inactivated fetal bovine serum, 2 mM L-glutamine, and 5 U/ml penicillin-5 mg/ml streptomycin in adherent cell culture conditions at 37°C with 5% CO2.

extract_protocol:
RNA extraction was conducted using the Quick-RNA Miniprep kit (Zymo Research), followed by RNA clean-up using the RNA Clean & Concentrator-5 kit (Zymo Research).
Library preparation was done using the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research).
Libraries were sequenced on an Illumina NovaSeq 6000 instrument with a sequencing depth of 30 million read pairs.

treatment_protocol: CFBE41o- cells were apically treated with fluorescently labeled phages OMKO1, LPS-5, PSA04, and PSA34 at a concentration of 1 x 109 PFU/ml in MEM pH-adjusted to 6.5 for 24 h.

value: Bronchial epithelium

tag: cell line

tag: cell type

value: Bronchial epithelial cells

value: CFTR deltaF508/deltaF508


title: HGA113

description: Sample 154


title: Cerebellum, ChIP, replicate 3


title: ED211124_t

description: total RNA

data_processing:
Transcritpomic dataset: Sequencing reads in FASTQ files were aligned to a reference transcriptome (mm10-2.1.0) and collapsed into unique molecular identifier counts using the 10x Genomics Cell Ranger software (version 3.0.2 and 5.0.1).Data were read into R (version 3.6.0) as a count matrix and cells wer filtered using Seurat v3 with cut-offs for: max/min gene expression, max nCount_RNA, and percentage of total reads that aligned to the mitochondrial genome (applied cut-offs see Supplementary Data 1, Bandler et al. 2021).
Filtered count matrix
Assembly: mm10-2.1.0

source_name: Transcriptomic dataset of tCROP-seq


title: LPS-5_1


title: Cerebellum, ChIP, replicate 2


title: ED211111_t

description: total RNA


title: OMKO1_3


title: HGA112

description: Sample 153


title: ED210415_t

description: total RNA

source_name: Transcriptomic dataset of tCROP-seq in cortex


title: HGA111

description: Sample 152


title: PSA34_1


title: OMKO1_2


title: Cerebellum, ChIP, replicate 1


title: Liver, Input

source_name: Liver

value: Liver


title: HGA109

description: Sample 151


title: PSA04_1


title: Liver, ChIP, replicate 2


title: ED210215_t

description: total RNA


title: ED201020_t

description: total RNA


title: HGA105

description: Sample 149


title: Liver, ChIP, replicate 1


title: ED201006_t

description: total RNA


title: HGA106

description: Sample 150


title: Dentate gyrus granule cells, ChIP, replicate 2

source_name: Hippocampus

value: Hippocampus

value: Dentate gyrus granule cells

value: Polr3a cKI/+, Rbp4-Cre


title: OMKO1_1


title: ED200806_t

description: total RNA


title: HGA083

description: Sample 147


title: Untreated_1

value: Untreated


title: HGA084

description: Sample 148


title: Multiplexed cells, scRNA Seq

city: Homburg

first: Felix

last: Ritzmann

address: Kirrberger Street

institute: Saarland University

description: BD Rhapsody

data_processing:
Raw data were processed and mapped by the BD Rhapsody™ WTA Analysis Pipeline on the sevenbridges platform.
Assembly: GRCh38-PhiX-gencodev29
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Cells from organoid cultures were collected by TrypLE detachment, washed in PBS w/o Mg_Ca, resuspended in BD Rhapsody Buffer
BD Rhapsody Library construction, according to manufacturer's instructions

value: Lung

value: untreated


title: Dentate gyrus granule cells, ChIP, replicate 1


title: Epi_N2

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

institute: TUD Dresden University of Technology

description: biological replicate 3

data_processing:
bcl2fastq2 2.20.0
Adapters (nextera:CTGTCTCTTATA) and polyA/T tails were trimmed with cutadapt (v2.6)[12] and pairs where one or both reads were shorter than 35bp were removed
Fragments were aligned to the mouse reference genome GRCm39 using the aligner gsnap (v2020-12-16) with Ensembl 104 mouse splice sites as support
Uniquely mapped fragments were assigned to genes based on their overlap to Ensembl 104 mouse gene annotations using featureCounts (v2.0.1)
Assembly: mus musculus GRCm39
Supplementary files format and content: bfx1989.GRCm39.e104.annotated.xlsx
Supplementary files format and content: spreadsheet where each row represents a gene and each column either gene information (e.g. start- and end coordinate, chromosome, strand) or the fragments counts per gene per sample

source_name: E14.5, neocortex

extract_protocol:
RNA was extracted using the Quick-RNA FFPE MiniPrep kit.
Transcriptome libraries were prepared using the SmartSeq 2 protocol (Picelli et al., 2013).

treatment_protocol: Mouse brain hemispheres were cultured under rotation conditions (HERO) either without (control) or with 50 ng/mL human recombinant EPIREGULIN.

value: E14.5, neocortex

value: neuron, N

value: wild-type

value: EPIREGULIN

value: 24 hours


title: ED210204_t

description: total RNA

value: Forebrain

value: FACSorted for GFP


title: Control participant #2

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

description: 10X Genomics

data_processing:
Sequence reads from all samples were processed and aggregated using a Cell Ranger (version 6.0)
Supplementary files format and content: hg38
Supplementary files format and content: tab-separated files and matrix files

source_name: Submandibular gland

extract_protocol:
Human submandibular gland biopsy samples were dissociated by a gentleMACS octo dissociator. Digested submandibular gland cells in cell suspension were separated using Percoll solution. Subsequently, submandibular gland cells were stained with anti-human CD45 PE and non-hematopoietic cells (CD45-) were purified from stained cells using a FACS cell sorting system (BD Aria III) and then encapsulated in droplets.
Libraries were then prepared using Chromium Single Cell 3’ Reagent Kits v3.1 following the manufacturer’s protocol. The generated scRNA-seq libraries were sequenced using a total of 127 cycles (paired-end reads) with a NovaSeq 6000 using NovaSeq 6000 S1 Reagent 100 Cycles Kit.

value: Submandibular gland


title: Epi_N1

description: biological replicate 2


title: Layer V cortical neurons, Input

description: tags_Rbp4-Cre_Polr3a-cK_Cprtex_ChIP_343430_S18_R1_001.genome.bowtie2.ucsc.bigWig

source_name: Cortex

value: Cortex

value: Layer V cortical neurons


title: HGA077

description: Sample 145

value: HGG


title: Untreated_2

value: Bronchial epithelium

value: Bronchial epithelial cells

value: CFTR deltaF508/deltaF508


title: IgG4-RD patient #2

description: 10X Genomics


title: Layer V cortical neurons, ChIP, replicate 2

value: FLAG (Sigma, F1804)

value: Polr3a cKI/+, Rbp4-Cre


title: HGA082

description: Sample 146


title: HGA071

description: Sample 144


title: Dentate gyrus granule cells, Input

description: 343426_Rbp4_H_S21_R1_001.genome.bowtie2.ucsc.bigWig

value: Hippocampus

value: Dentate gyrus granule cells


title: Layer V cortical neurons, ChIP, replicate 1


title: HGA068

description: Sample 143


title: Ctl_N2

description: biological replicate 3

value: E14.5, neocortex

value: neuron, N

value: control


title: Control participant #1

description: 10X Genomics


title: HGA064_T2

description: Sample 142


title: Pericytes, Input

description: tags_PdgfrB-Cre_Polr3a-cKI_ChIP_336062_S21_R1_001.genome.bowtie2.ucsc.bigWig

value: Pericytes

value: Polr3a cKI/+, Pdgfrb-Cre


city: Milan

first: Serena

last: Ghisletti

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description:
Cfpac1 cells, Trametinib 24h, ELF3 Knockout 2
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

data_processing:
Fastq raw reads were processed with FASTQC tool v0.11.9 for quality base check and to exclude any technical bias in the data. Sequences were then checked for the presence of the adaptors using trimmomatic_v0.39. Trimmed single-end reads were then mapped onto the human genome GRCh38 assembly version using STAR-v.2.7.8a (PMID 23104886) with the following parameters: --limitSjdbInsertnsJ = 500,000, --alignIntronMax=1,000,000, --alignIntronMin=20. After uniquely mapped reads were retained, gene counts were retrieved using featureCounts on Gencode GRCh38 annotation (Ensembl 104 version). Next, protein-coding genes were selected and processed with the edgeR_3.39 R-package (PMID 19910308) for gene filtering, normalization and differential testing. Differentially expressed genes were defined using the following thresholds: absolute log Fold-Change value > 1 and FDR < 0.001.
Repetitive element analysis: RNAseq data were aligned onto the hg38 genome using STAR-v.2.7.8a with the following settings: --outFilterMultimapNmax 500 –winAnchorMultimapNmax 500. For the read count estimation, repeats were quantified using TEtranscript (PMID 26206304) in the ‘multi’ mode using the same gene annotation (GTF file) in primary RNA-seq analysis and a UCSC-RepeatMasker (v-4.1.1) GTF for the TE-annotation. Subfamily-level counts were processed with edgeR_v3.39 for data normalization and differential testing. Differentially-expressed subfamilies were defined by setting absolute log(Fold-Change) threshold of 1 and FDR < 0.05.
For the Cfpac1-ELF3KO data set, repetitive element analysis was performed using the same computational workflow described in the previous section.
Assembly: GRCh38 assembly version
Supplementary files format and content: tab-delimited files include gene-level normalized CPM values for each cell line.
Supplementary files format and content: tab-delimited files include CPM values of repeat subfamilies for each cell line.
Supplementary files format and content: Normalized coverage data are provided in BigWig format.

molecule: polyA RNA

growth_protocol: Cells were maintained in Iscove's Modified Dulbecco's Medium (IMDM) +10% fetal bovine serum (FBS) (CFPAC-1), RPMI+15% FBS (CAPAN-2), Dulbecco's Modified Eagle Medium+10% FBS (MiaPaca-2, PANC-1, HEK293T). Media were all supplemented with 2 mM L-glutamine.

extract_protocol:
Total RNA from was extracted using the Quick-RNA Miniprep Kit (Zymo Research, R1055)
RNA-seq was carried out using the SMART-seq2 protocol (PMID 24385147) with minor modifications, as described (PMID 35568393)
Single-end and Paired-end RNAseq

treatment_protocol: Trametinib (Selleckchem S2673) was diluted in DMSO and used at a concentration of 20 nM for all the experiments. Cells were plated in 96 well, 24 well, 6 well or 10 cm plates 24-48 h before treatment and treated for the indicated time at the reported concentration of drugs directly diluted in their own medium

value: PDAC Low-grade

value: ELF3 KO

value: Trametinib 24h


title: Ctl_N1

description: biological replicate 2

value: wild-type

value: 24 hours


description:
Cfpac1 cells, Trametinib 24h, ELF3 Knockout 1
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt


title: Pericytes, ChIP, replicate 2

value: Cortex


title: HGA064_T1

description: Sample 141

value: HGG


title: Pericytes, ChIP, replicate 1


title: HGA057

description: Sample 140


description:
Cfpac1 cells, Untreated, ELF3 Knockout 2
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: Untreated


title: Inhibitory interneurons, Input

description: 339593_Dlx_S23_R1_001.genome.bowtie2.ucsc.bigWig

value: Inhibitory interneurons

value: Polr3a cKI/+, Dlx6a-Cre


title: Epi_IP1

description: biological replicate 2

value: intermediate progenitor, IP

value: EPIREGULIN


title: IgG4-RD patient #1

description: 10X Genomics

value: Submandibular gland


title: Epi_IP2

description: biological replicate 3

value: E14.5, neocortex


title: Epi_IP

description: biological replicate 1


title: Cfpac1 cells, Trametinib 24h, WT6

description:
Cfpac1 cells, Trametinib 24h, WT6
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: Wild type


title: HGA056

description: Sample 139


title: HGA053

description: Sample 138


title: Cfpac1 cells, Trametinib 24h, WT5

description:
Cfpac1 cells, Trametinib 24h, WT5
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt


title: Inhibitory interneurons, ChIP, replicate 1

value: Hippocampus

value: FLAG (Sigma, F1804)


title: Epi_N

description: biological replicate 1

value: neuron, N


title: Cfpac1 cells, Trametinib 24h, WT4

description:
Cfpac1 cells, Trametinib 24h, WT4
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: PDAC Low-grade


title: Oligodendrocyes, Input

value: Cerebellum

value: Cerebellar oligodendrocytes

value: Polr3a cKI/+, Plp1-Cre


title: Ctl_IP1

description: biological replicate 2

value: wild-type

value: control

value: 24 hours


title: HGA025

description: Sample 137

value: HGG


title: Ctl_N

description: biological replicate 1


title: Ctl_IP

description: biological replicate 1


title: Cfpac1 cells, Trametinib 24h, WT3

description:
Cfpac1 cells, Trametinib 24h, WT3
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: Trametinib 24h


description:
Cfpac1 cells, Untreated, ELF3 Knockout 1
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: ELF3 KO

value: Untreated


title: HGA023

description: Sample 135


title: Epi_RG2

description: biological replicate 3

value: radial glia, RG

value: EPIREGULIN


title: Inhibitory interneurons, ChIP, replicate 2

value: Inhibitory interneurons

value: Polr3a cKI/+, Dlx6a-Cre


title: Midbrain dopaminergic neurons, Input

source_name: Midbrain

value: Midbrain

value: Midbrain dopaminergic neurons

value: Polr3a cKI/+, DAT-Cre


title: HGA022

description: Sample 134


title: Epi_RG1

description: biological replicate 2

value: E14.5, neocortex


title: Cfpac1 cells, Untreated, WT6

description:
Cfpac1 cells, Untreated, WT6
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: PDAC Low-grade

value: Wild type


title: Epi_RG

description: biological replicate 1

value: wild-type


title: Cfpac1 cells, Trametinib 24h, WT1

description:
Cfpac1 cells, Trametinib 24h, WT1
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt


title: Ctl_IP2

description: biological replicate 3

value: intermediate progenitor, IP

value: control


title: Midbrain dopaminergic neurons, ChIP, replicate 1

value: FLAG (Sigma, F1804)


title: Midbrain dopaminergic neurons, ChIP, replicate 2


title: Cfpac1 cells, Untreated, WT5

description:
Cfpac1 cells, Untreated, WT5
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt


title: HGA016

description: Sample 131

value: HGG


title: HGA024

description: Sample 136


title: Spinal cord motor neurons, Input

source_name: Spinal cord

value: Spinal cord

value: Cholinergic (motor) neurons

value: Polr3a cKI/+, ChAT-Cre


title: HGA015

description: Sample 130


title: Ctl_RG2

description: biological replicate 3

value: radial glia, RG

value: 24 hours


title: Oligodendrocytes, ChIP, replicate 2

value: Cerebellum

value: Cerebellar oligodendrocytes

value: Polr3a cKI/+, Plp1-Cre


title: Ctl_RG1

description: biological replicate 2


title: Cfpac1 cells, Trametinib 24h, WT2

description:
Cfpac1 cells, Trametinib 24h, WT2
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: Trametinib 24h


title: HGA014

description: Sample 129


title: Ctl_RG

description: biological replicate 1

value: E14.5, neocortex


title: Spinal cord motor neurons, ChIP, replicate 1


title: HGA018

description: Sample 132


title: HGA020

description: Sample 133

value: MMRD HGG


title: Cfpac1 cells, Untreated, WT1

description:
Cfpac1 cells, Untreated, WT1
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: PDAC Low-grade

value: Wild type

value: Untreated


title: Oligodendrocytes, ChIP, replicate 1


title: ARID1A_ATAC_KO4

city: Chapel hill

first: Terry

last: Magnuson

state: NC

address: 120 Mason Farm Road, Genetics Medicine Bldg.,

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
ATAC_lib8
AvgMUT_ATAC.bw
MUT_ATACblfilt_overlap.bed

data_processing:
Reads were trimmed for adapter sequences and N's form either side using TrimGalore
Alignment to the mm10 genome was performed using bowtie2.
Alignments were outputted to BAM format using samtools and PCR duplicates were filtered out using Picard tools - MarkDuplicates
BAM files were converted to bigWig format which were filtered for mm10 ENCODE excluded regions, using Deeptools - bamCoverage
Replicate bigWIg were averaged using WiggleTools
Assembly: mm10
Supplementary files format and content: BED files listing ATAC-seq MACS2 peak calls.
Supplementary files format and content: bigwig files

source_name: Pachytene spermatocytes

extract_protocol:
ATAC-seq samples were prepared using standard Omni-ATAC protocol. Transposed DNA was purified using Zymo DNA clean and concentrator kit (catalog no. D4014)
Sequencing libraries were prepared from transposed DNA containing nextera adapters as specified in Omni-ATAC protocol.

value: Pachytene spermatocytes


title: Spinal cord motor neurons, ChIP, replicate 2

value: FLAG (Sigma, F1804)


title: ARID1A_ATAC_KO3

description:
ATAC_lib7
AvgMUT_ATAC.bw
MUT_ATACblfilt_overlap.bed


title: Cfpac1 cells, Untreated, WT2

description:
Cfpac1 cells, Untreated, WT2
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt


title: HGA011

description: Sample 127

value: HGG


title: Microglia, ChIP, replicate 1

value: Cortex

value: Microglia

value: Polr3a cKI/+, Tmem119-Cre


title: ARID1A_ATAC_KO2

description:
ATAC_lib6
AvgMUT_ATAC.bw
MUT_ATACblfilt_overlap.bed


title: Microglia, ChIP, replicate 2


title: HGA009

description: Sample 126


description:
Panc1 cells, RNAseq Trametinib 24h, Rep3
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt

value: PDAC High-grade


description:
Panc1 cells, RNAseq Trametinib 24h, Rep4
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: Cfpac1 cells, Untreated, WT3

description:
Cfpac1 cells, Untreated, WT3
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt


description:
Panc1 cells, RNAseq Trametinib 24h, Rep2
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: ARID1A_ATAC_WT4

description:
ATAC_lib4
AvgWT_ATAC.bw
WT_ATACblfilt_overlap.bed


title: Astrocyes, Input

value: Astrocytes

value: Polr3a cKI+, Aldh1l1-Cre


title: HepG2, non-treated, nanopore sequencing, biological replicate1

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

description: Discover the full-length non-capped RNAs of the mammalian transcriptome

data_processing:
NGS raw data gained from Illumina HiSeqX10 with 150 bp paired end reads, TGS raw data gained from MinION nanopore with single end reads
For Illumina sequencing data, Cutadapt (v2.8) (Martin, 2011) was firstly used to cut the sequencing adapters of the paired-end reads with the following parameters: cutadapt -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGT -m 15 -e 0.15. The NAP-seq specific 5’-adapter (AAGCAGTGGTATCAACGCAGAGT) and 3’-adapter (AGTCGTAGTAAGTCTGTGCTCG) which marked the boundary of the napRNAs were subsequently moved by our programme flClipAdapter with the following parameters: -l 15 -e 0.1 -c 6. Finally, the reads were mapped to the reference genome (hg38 or mm10) with STAR (Dobin et al., 2013) software with the following parameters: --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20  --outFilterMatchNminOverLread 0.8  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat .   For nanopore sequencing data, Cutadapt (v2.8) was used to cut the NAP-seq specific adapters with the following parameters: -j 16 -g AAGCAGTGGTATCAACGCAGAGT -a AGTCGTAGTAAGTCTGTGCTCG -m 20 -e 0.3 -O 10, and then use Cutadapt again to move any possible adapters with the following parameters: -j 16 -g CGAGCACAGACTTACTACGACT -a ACTCTGCGTTGATACCACTGCTT -m 20 -e 0.3 -O 10, and we just retained the read that contained the NAP-seq specific adapters. Finally, thr reads were mapped to the reference genome (hg38) with minimap2 (Li, 2018) with the following parameters: --junc-bed hg38.gencode.v30.geneAnno.bed -t 16 -k15 -w5 --splice -g2000 -G200k -A2 -B4 -O4,96 -E2,0 -C18 -z400,200 -ub --end-bonus=18 --junc-bonus=18 --splice-flank=yes -ub --sam-hit-only --secondary=no -a
To identify pronounced high-confidence napRNAs, we firstly assembled the continuous reads to the contigs, and then calculated the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We reasoned that the startReadNum and endReadNum of a candidate napRNA should be significantly higher over the sequence upstream and downstream, while the coverage of the contigs should also be significantly higher over the regions around.  Finally, we developed the computational software napSeeker to calculate the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We calculated the fold change between startReadNum and numbers of reads containing specific 5’-adapter within 100nt upstream and downstream (startFC), in a similar way, the fold change between endReadNum and the numbers of reads containing specific 3’-adapter upstream and downstream within 100nt (endFC). Next, we calculated the fold change between coverage of the contigs and the regions within 20nt upstream/downstream (up20ntFC/down20ntFC).  A high-confidence napRNA had to meet the following criteria: (1) startReadNum, endReadNum ≥ 7; (2) startFold, endFold ≥ 2. (2) up20ntFold, down20ntFold ≥ 2. (4) length≥100. What’s more, the candidate napRNAs had to express in at least 2 samples of all the human (or mouse) samples. Finally, we only retained the napRNA with the summary counts ≥ 20. These stringent parameters allowed us to identify the highest-confidence candidate napRNAs.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: bigwig files were generated using self-developed software; Scores represent Reads per million mapped reads (RPM).

source_name: Human hepatocellular carcinoma cells

growth_protocol: HepG2 and U-87 MG were cultured in MEM supplemented with 10% FBS, 1% penicillin-streptomycin at 37 °C in a humidified. HEK293T and C2C12 cells were clutured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere with 95% air and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. 2ug total RNA was used to prepare the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina or nanopore protocols

treatment_protocol: HepG2 cells were treated with 500ng/ml ADR or 500μM CoCl2 for 24h before harvesting; 2ug/ml poly (I:C) were transfected into HepG2 with lipo2000 and then the cells were cultured for 12h before harvesting. C2C12 cells grow up to 80% confluence, and then the culture medium was changed to the differentiation medium which is consisted of DMEM with 2% horse serum.

value: non-treated

tag: treatment label

value: wild type

tag: molecule subtype

value: total RNA, remove rRNA


title: HGA013

description: Sample 128


title: DMG157

description: Sample 124


description:
Panc1 cells, RNAseq Trametinib 24h, Rep1
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt

value: Trametinib 24h


title: ARID1A_ATAC_KO1

description:
ATAC_lib5
AvgMUT_ATAC.bw
MUT_ATACblfilt_overlap.bed


title: Astrocytes, ChIP, replicate 2


title: DMG156

description: Sample 123


title: Microglia, Input


title: ARID1A_ATAC_WT3

description:
ATAC_lib3
AvgWT_ATAC.bw
WT_ATACblfilt_overlap.bed


title: ARID1A_ATAC_WT2

description:
ATAC_lib2
AvgWT_ATAC.bw
WT_ATACblfilt_overlap.bed


description:
Panc1 cells, RNAseq Trametinib 12h, Rep4
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt

value: Trametinib 12h


title: Astrocytes, ChIP, replicate 1


title: Purkinje cells, Input

value: Cerebellum

value: Purkinje cells

value: Polr3a cKI/+, Pcp2-Cre


title: ARID1A_ATAC_WT1

description:
ATAC_lib1
AvgWT_ATAC.bw
WT_ATACblfilt_overlap.bed

value: Pachytene spermatocytes


description:
Panc1 cells, RNAseq Trametinib 12h, Rep3
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt

value: Wild type


title: DMG151

description: Sample 122

value: HGG


description:
Panc1 cells, RNAseq Trametinib 12h, Rep2
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: DIPG143_T

description: Sample 121


title: ARID1A_RNA-seq_KO4

description:
RNA-seq_lib8
ARID1A_DeSeq2_DEG_list.txt

data_processing:
Quantification of gene expression was performed using Salmon
Gene level counts were summarized using tximport and then imported to perform differential gene expression analysis using DESeq2
Low-count genes (< 10 reads) were pre-filtered and significant differences in counts were called at a false discovery rate (FDR≤ 0.05).
Assembly: mm10
Supplementary files format and content: txt file listing differentially expressed genes (FDR≤ 0.05) with corresponsing log fold changes

extract_protocol:
RNA was extracted in TRIzolTM reagent (Invitrogen, 15596026) from biological replicates of Arid1aWT and Arid1acKO pachytene spermatocytes replicates and purified using the Direct-zol RNA kit (Zymo, R2050). All samples displayed RNA integrity number (RIN)  > 7.0 as determined by Agilent Tapestation (High sensitivity RNA screen tape).
Sequencing libraries were prepared from 1 µg of total RNA using a Kapa mRNA HyperPrep kit (Roche, KK8580)


title: Purkinje cells, ChIP, replicate 2

value: FLAG (Sigma, F1804)


title: DMG162

description: Sample 125


title: ARID1A_RNA-seq_KO3

description:
RNA-seq_lib7
ARID1A_DeSeq2_DEG_list.txt


title: Purkinje cells, ChIP, replicate 1


title: DIPG134

description: Sample 120


title: DIPG133

description: Sample 119


description:
Panc1 cells, RNAseq Trametinib 12h, Rep1
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: Cfpac1 cells, Untreated, WT4

description:
Cfpac1 cells, Untreated, WT4
Pdac.CFPAC1.ELF3KO.expData.repElements.normalizedCounts.txt

value: PDAC Low-grade

value: Untreated


title: Panc1 cells, RNAseq Trametinib 3h, Rep4

description:
Panc1 cells, RNAseq Trametinib 3h, Rep4
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt

value: PDAC High-grade

value: Trametinib 3h


title: DIPG132_T

description: Sample 118


title: Cerebellar granule cells, ChIP, replicate 2

value: Cerebellar granule cells

value: Polr3a cKI/+, Gabra6-Cre


title: ARID1A_RNA-seq_KO1

description:
RNA-seq_lib5
ARID1A_DeSeq2_DEG_list.txt


title: Cerebellar granule cells, Input


title: Panc1 cells, RNAseq Trametinib 3h, Rep3

description:
Panc1 cells, RNAseq Trametinib 3h, Rep3
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: ARID1A_RNA-seq_KO2

description:
RNA-seq_lib6
ARID1A_DeSeq2_DEG_list.txt


title: Panc1 cells, RNAseq Trametinib 3h, Rep2

description:
Panc1 cells, RNAseq Trametinib 3h, Rep2
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: Cerebellar granule cells, ChIP, replicate 1


title: ARID1A_RNA-seq_WT4

description:
RNA-seq_lib4
ARID1A_DeSeq2_DEG_list.txt


title: ARID1A_RNA-seq_WT3

description:
RNA-seq_lib3
ARID1A_DeSeq2_DEG_list.txt


title: DIPG127_T

description: Sample 117


title: DIPG119_AUT

description: Sample 114


title: ED210215_g

description: CRISPR RNA

data_processing:
N/A
Assembly: mm10-2.1.0

source_name: Guide dataset of ED210215

value: Forebrain

value: FACSorted for GFP


title: DIPG122

description: Sample 116


title: ARID1A_RNA-seq_WT2

description:
RNA-seq_lib2
ARID1A_DeSeq2_DEG_list.txt


title: Panc1 cells, RNAseq Trametinib 3h, Rep1

description:
Panc1 cells, RNAseq Trametinib 3h, Rep1
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: Panc1 cells, RNAseq Untreated, Rep3

description:
Panc1 cells, RNAseq Untreated, Rep3
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: DIPG119_T

description: Sample 115


title: ARID1A_RNA-seq_WT1

description:
RNA-seq_lib1
ARID1A_DeSeq2_DEG_list.txt


title: ED201006_g

description: CRISPR RNA

source_name: Guide dataset of ED201006


title: H3-3_CnR_KO3

description:
CnR_lib17
MUT_H3-3commonPks_rel2rabIgG.bed
AvgMUT_H3-3_cnr.bw

data_processing:
library strategy: CUT&RUN
Reads were trimmed for adapter sequences and N's form either side using TrimGalore
Alignment to the mm10 genome was performed using bowtie2.
Alignments were outputted to BAM format using samtools and PCR duplicates were filtered out using Picard tools - MarkDuplicates
BAM files were converted to bigWig format which were filtered for mm10 ENCODE excluded regions, using Deeptools - bamCoverage
Replicate bigWIg were averaged using WiggleTools
Assembly: mm10
Supplementary files format and content: BED files listing H3.3 MACS2 peak calls.
Supplementary files format and content: bigwig files

extract_protocol:
Aliquots of cryopreserved Arid1aWT and Arid1acKO  pachytene spermatocytes were quickly thawed in a water bath at room temperature (RT), pelleted at 600g for 5 minutes, and washed [wash buffer: 20mM HEPES(Na) pH7.5, 150 mM NaCl, 0.5 mM spermidine, EDTA-free protease inhibitor] three times. Cells were gently resuspended in wash buffer and bound to Concanavalin-A coated magnetic beads (20 µL beads/500,000 cells) by mixing on a rotator for 15 minutes. The bead slurry was separated using a magnet followed by permeabilization in 50 µL antibody buffer (wash buffer + 0.05% Digitonin + 2mM EDTA) per sample in 0.2 mL 8-strip PCR tubes. Primary antibody was added to the samples and incubated on a nutator at 4 oC overnight. Cells were then separated using a magnet, washed two times in 200 µL Dig-wash buffer (wash buffer + 0.05% Digitonin), and incubated with a secondary antibody prepared in 50 µL of Dig-wash buffer/sample for 30 minutes on a nutator at 4 oC. After antibody incubations, samples were washed twice in 200 µL Dig-wash buffer and then incubated on a nutator at 4 oC with 50 µL Dig-wash buffer containing 1000ng/mL Protein A/G Micrococcal Nuclease (pA/G-MNase) for 1 hr. Following this, samples were washed twice in 200 µL Dig-wash buffer, resuspended in 50 µL Dig-wash buffer, cooled down to 0 oC, and supplemented with CaCl2 at a final concentration of 2 mM to activate MNase. Samples were digested at 0 oC for 40 minutes. The resulting chromatin fragments were extracted from the bead slurry by incubating in 2X STOP buffer (340 mM NaCl, 20mM EDTA, 4mM EGTA, 0.05% Digitonin, 100 µg/mL RNase A) at 37 oC for 30 minutes. DNA was purified using ChIP DNA clean and concentrator kit (Zymo, D5205).
Libraries were created using Kapa hyperprep kit (Roche catalog no.  KK8504) for Illumina sequencing.

value: anti-H3.3 antibody


title: Panc1 cells, RNAseq Untreated, Rep1

description:
Panc1 cells, RNAseq Untreated, Rep1
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: ED200806_g

description: CRISPR RNA

source_name: Guide dataset of ED200806


title: ED210204_g

description: CRISPR RNA

source_name: Guide dataset of ED210204


title: ED201020_g

description: CRISPR RNA

source_name: Guide dataset of ED201020


title: DIPG115_T

description: Sample 113

source_name: pediatric brain tumor


title: ED200630_g

description: CRISPR RNA

source_name: Guide dataset of ED200630


title: DIPG109_T

description: Sample 112


title: H3-3_CnR_WT2

description:
CnR_lib14
WT_H3-3commonPks_rel2rabIgG.bed
AvgWT_H3-3_cnr.bw


title: Panc1 cells, RNAseq Untreated, Rep2

description:
Panc1 cells, RNAseq Untreated, Rep2
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


description:
MiaPaca2 cells, RNAseq Trametinib 24h, Rep3
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt

value: Trametinib 24h


title: H3-3_CnR_KO2

description:
CnR_lib16
MUT_H3-3commonPks_rel2rabIgG.bed
AvgMUT_H3-3_cnr.bw


title: DIPG099_T

description: Sample 110


description:
MiaPaca2 cells, RNAseq Trametinib 24h, Rep4
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: DIPG097_T

description: Sample 108


title: ARID1A_CnR_SIGMAantibody_cKO3

description:
CnR_lib12
AvgMUT_Sigma_cnr.bw

value: anti-ARID1A antibody (Sigma)


description:
MiaPaca2 cells, RNAseq Trametinib 12h, Rep4
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt

value: Trametinib 12h


title: ED200804_g

description: CRISPR RNA

source_name: Guide dataset of ED200804


description:
MiaPaca2 cells, RNAseq Trametinib 24h, Rep1
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: Panc1 cells, RNAseq Untreated, Rep4

description:
Panc1 cells, RNAseq Untreated, Rep4
Pdac.PANC1.genes.normalizedCounts.txt
Pdac.PANC1.repElements.normalizedCounts.txt


title: ED200526_g

description: CRISPR RNA

source_name: Guide dataset of ED200526


description:
MiaPaca2 cells, RNAseq Trametinib 24h, Rep2
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: H3-3_CnR_WT1

description:
CnR_lib13
WT_H3-3commonPks_rel2rabIgG.bed
AvgWT_H3-3_cnr.bw


title: DIPG098_T

description: Sample 109


title: H3-3_CnR_KO1

description:
CnR_lib15
MUT_H3-3commonPks_rel2rabIgG.bed
AvgMUT_H3-3_cnr.bw


title: ED191217_g

description: CRISPR RNA

source_name: Guide dataset of ED191217


title: ED200218_g

description: CRISPR RNA

source_name: Guide dataset of ED200218


title: ED200211_g

description: CRISPR RNA

source_name: Guide dataset of ED200211


title: DIPG096_T

description: Sample 107


title: DIPG100_T

description: Sample 111


description:
MiaPaca2 cells, RNAseq Trametinib 12h, Rep2
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: ED190203_g

description: CRISPR RNA

source_name: Guide dataset of ED190203


title: DIPG095_T

description: Sample 106


title: ARID1A_CnR_SIGMAantibody_cKO1

description:
CnR_lib10
AvgMUT_Sigma_cnr.bw


title: ARID1A_CnR_SIGMAantibody_WT3

description:
CnR_lib9
AvgWT_Sigma_cnr.bw


description:
MiaPaca2 cells, RNAseq Trametinib 12h, Rep3
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: DIPG094_T

description: Sample 105


title: ED210215_b

description: lineage barcode RNA

source_name: Barcode dataset of ED210215


description:
MiaPaca2 cells, RNAseq Trametinib 3h, Rep4
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: DIPG091_T

description: Sample 102


title: DIPG093_T

description: Sample 104


description:
MiaPaca2 cells, RNAseq Trametinib 12h, Rep1
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: ARID1A_CnR_CSTantibody_cKO3

description:
CnR_lib6
AvgMUT_CST_cnr.bw

value: anti-ARID1A antibody (Cell signaling technologies)


title: ED210204_b

description: lineage barcode RNA

source_name: Barcode dataset of ED210204


title: ARID1A_CnR_SIGMAantibody_cKO2

description:
CnR_lib11
AvgMUT_Sigma_cnr.bw

source_name: Pachytene spermatocytes

value: Pachytene spermatocytes


title: ARID1A_CnR_SIGMAantibody_WT2

description:
CnR_lib8
AvgWT_Sigma_cnr.bw


title: DIPG092_T

description: Sample 103


title: ARID1A_CnR_SIGMAantibody_WT1

description:
CnR_lib7
AvgWT_Sigma_cnr.bw


title: ARID1A_CnR_CSTantibody_cKO2

description:
CnR_lib5
AvgMUT_CST_cnr.bw


description:
MiaPaca2 cells, RNAseq Trametinib 3h, Rep3
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt

value: Wild type


title: ED201013_t

description:
total RNA
Illumina NextSeq 500/ Illumina NovaSeq6000

source_name: Transcriptomic dataset of tCROP-seq


title: DIPG090_T

description: Sample 101

value: HGG


description:
MiaPaca2 cells, RNAseq Trametinib 3h, Rep2
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: ED200804_t

description: total RNA


title: ED200630_t

description: total RNA


title: DIPG089_T

description: Sample 100


description:
MiaPaca2 cells, RNAseq Trametinib 3h, Rep1
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: ARID1A_CnR_CSTantibody_cKO1

description:
CnR_lib4
AvgMUT_CST_cnr.bw


title: MiaPaca2 cells, RNAseq Untreated, Rep4

description:
MiaPaca2 cells, RNAseq Untreated, Rep4
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: DIPG088_T

description: Sample 99


title: ED200526_t

description: total RNA


title: DIPG086

description: Sample 98


title: MiaPaca2 cells, RNAseq Untreated, Rep3

description:
MiaPaca2 cells, RNAseq Untreated, Rep3
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: ED200218_t

description: total RNA


title: DIPG085_AUT

description: Sample 97


title: MiaPaca2 cells, RNAseq Untreated, Rep2

description:
MiaPaca2 cells, RNAseq Untreated, Rep2
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: ED191217_t

description: total RNA


title: ARID1A_CnR_CSTantibody_WT1

description:
CnR_lib1
AvgWT_CST_cnr.bw


title: MiaPaca2 cells, RNAseq Untreated, Rep1

description:
MiaPaca2 cells, RNAseq Untreated, Rep1
Pdac.MiaPaca2.genes.normalizedCounts.txt
Pdac.MiaPaca2.repElements.normalizedCounts.txt


title: DIPG082_T

description: Sample 96


title: DIPG078_T

description: Sample 95


title: DIPG071_T

description: Sample 94


title: scRNA_K

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

data_processing:
Cellranger 3.0
Seurat 4.0
Slingshot 2.4.0
Assembly: mm10
Supplementary files format and content: cellranger 3.0 barcode / features / matrix files
Supplementary files format and content: Seurat object with all cells and celltype metadata
Supplementary files format and content: Table of cells used for pseudotime with pseudotime values and deciles

source_name: spleen

extract_protocol:
B220+IgD- cells are sorted from spleens of SRBC-immunized mice by FACS.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit according to 10x Genomics specifications.

treatment_protocol: Mice (WT, C, K, and CK) were immunized with SRBC for 10 days before sorting splenic B220+IgD- cells.

value: spleen


title: Cfpac1 cells, ChIPseq ELF3, Trametinib 24h, Rep2

data_processing:
Reads were processed using Trimmomatic v0.39. Next, high-quality trimmed reads were aligned onto the human genome build GRCh38/hg38 using Shortstack v3.8.5 (PMID 23610128) with the following settings: --mismatches 2 --bowtie_m 100 --align_only --mmap u. Mapped reads were filtered to remove randomly placed multi-mappers and unmapped reads using samtools v1.16.9. Any alignment matching hg38-blacklist regions (https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz) was discarded using bedtools_v.2.30.0 (PMID 20110278) and duplicate reads removed with the samtools ‘markdup –r’ option. For the H3k27ac ChIP data, peaks were called using MACS2 v.2.2.7.1 (PMID 18798982) with the following parameters: --nomodel –extsize 250 –mfold 5 50 –broad –broad-cutoff 0.01. For the ELF3 ChIP data, we run MACS in ‘narrow-peak’ mode with parameters –nomodel –extsize 200 --mfold 5 50 -q 0.01.  H3K9me3 islands were called using Sicer2 v1.0.3 (PMID 19505939) with the following settings: --window_size=200 –fragment_size=300 -fdr=0.01 –gap_size=600. A corresponding input DNA from the same cell line was used as a control in peak detection in each data set.
Fragment pile-up in ‘Read Per Million’ were generated using MACS2 callpeak with parameters –format BAM –nomodel –B –SPMR, with the –extsize parameter set as the same used in the calling step. The resulting BedGraph files from ChIP was compared to that of the input to generate a signal profile in for data visualization in the genome browser (BigWig files).
Assembly: GRCh38 assembly version
Supplementary files format and content: Normalized coverage data are provided in BigWig format.

extract_protocol:
ChIP-seq was carried out as previously described (PMID 32997974) using 1x106 cells for the H3K27ac and H3K9me3 ChIP and 20×106 cells for the ELF3 ChIP. The following antibodies were used:  anti-H3K27ac (Abcam, ab4729), anti-H3K9me3 (Abcam, ab8898) and anti-ELF3 antibody (rabbit polyclonal antibody generated in-house using a peptide corresponding to aa1-150 of the human ELF3 reference protein sequence). DNA libraries were prepared as described (PMID 29706544) and sequenced on Illumina NextSeq 500 and NovaSeq6000 platforms.
All ChIPseq data sets were processed in single-end.

value: PDAC Low-Grade


title: scRNA_C


title: scRNA_CK


title: ED190203_t

description: total RNA

source_name: Transcritpomic datset of  tCROP-seq


title: Cfpac1 cells, ChIPseq ELF3, Trametinib 24h, Rep1


title: DIPG067_T

description: Sample 93


title: ARID1A_CnR_CSTantibody_WT3

description:
CnR_lib3
AvgWT_CST_cnr.bw


title: scRNA_WT

value: WT


title: Cfpac1 cells, ChIPseq ELF3, Untreated, Rep2

value: Untreated


title: HepG2_RNAseq_rep2

description:
HepG2, non-treated, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome

data_processing:
NGS raw data gained from Illumina HiSeqX10 with 150 bp paired end reads, TGS raw data gained from MinION nanopore with single end reads
For Illumina sequencing data, Cutadapt (v2.8) (Martin, 2011) was firstly used to cut the sequencing adapters of the paired-end reads with the following parameters: cutadapt -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGT -m 15 -e 0.15. The NAP-seq specific 5’-adapter (AAGCAGTGGTATCAACGCAGAGT) and 3’-adapter (AGTCGTAGTAAGTCTGTGCTCG) which marked the boundary of the napRNAs were subsequently moved by our programme flClipAdapter with the following parameters: -l 15 -e 0.1 -c 6. Finally, the reads were mapped to the reference genome (hg38 or mm10) with STAR (Dobin et al., 2013) software with the following parameters: --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20  --outFilterMatchNminOverLread 0.8  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat .     For nanopore sequencing data, Cutadapt (v2.8) was used to cut the NAP-seq specific adapters with the following parameters: -j 16 -g AAGCAGTGGTATCAACGCAGAGT -a AGTCGTAGTAAGTCTGTGCTCG -m 20 -e 0.3 -O 10, and then use Cutadapt again to move any possible adapters with the following parameters: -j 16 -g CGAGCACAGACTTACTACGACT -a ACTCTGCGTTGATACCACTGCTT -m 20 -e 0.3 -O 10, and we just retained the read that contained the NAP-seq specific adapters. Finally, thr reads were mapped to the reference genome (hg38) with minimap2 (Li, 2018) with the following parameters: --junc-bed hg38.gencode.v30.geneAnno.bed -t 16 -k15 -w5 --splice -g2000 -G200k -A2 -B4 -O4,96 -E2,0 -C18 -z400,200 -ub --end-bonus=18 --junc-bonus=18 --splice-flank=yes -ub --sam-hit-only --secondary=no -a    For SHAPE-MaP data, preprocessing of SHAPE-MaP sequencing data was the same as NAP-seq Illumina sequencing data, including remove the sequencing adapters and NAP-seq specific adapters. Then clean paired-end reads of three biological replicates were merge and mapped to each identified napRNAs. The alignments for individual napRNAs were extracted and processed with shapemapper_mutation_parser, shapemapper_mutation_counter and the python script make_reactivity_profiles.py from ShapeMapper2 to produce the reactivity profiles. The SHAPE reactivity profiles were used to guide RNA structure prediction using RNA RNAalifold. We further manually adjust the RNA structure for some polyA-pocket-ACA-napRNAs to make it more more consistent to the hairpin-pocket-hinge-hairpin structure.    For CAP-seq data, Cutadapt (v2.8) (Martin, 2011) was first used with the following parameters to remove the sequencing adapters from the paired-end reads: cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 3 -e 0.15. Then the reads were mapped to the reference genome (hg38) with STAR (Dobin et al., 2013) software.
To identify pronounced high-confidence napRNAs, we firstly assembled the continuous reads to the contigs, and then calculated the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We reasoned that the startReadNum and endReadNum of a candidate napRNA should be significantly higher over the sequence upstream and downstream, while the coverage of the contigs should also be significantly higher over the regions around.  Finally, we developed the computational software napSeeker to calculate the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We calculated the fold change between startReadNum and numbers of reads containing specific 5’-adapter within 100nt upstream and downstream (startFC), in a similar way, the fold change between endReadNum and the numbers of reads containing specific 3’-adapter upstream and downstream within 100nt (endFC). Next, we calculated the fold change between coverage of the contigs and the regions within 20nt upstream/downstream (up20ntFC/down20ntFC).  A high-confidence napRNA had to meet the following criteria: (1) startReadNum, endReadNum ≥ 7; (2) startFold, endFold ≥ 2. (2) up20ntFold, down20ntFold ≥ 2. (4) length≥100. What’s more, the candidate napRNAs had to express in at least 2 samples of all the human (or mouse) samples. Finally, we only retained the napRNA with the summary counts ≥ 20. These stringent parameters allowed us to identify the highest-confidence candidate napRNAs.  To identify the highest-confidence candidate 5’-Cap sites, we calculated the 5’-end sites coverage of the sequencing read (endCov), the one nucleotide upstream (upCov) and the one nucleotide downstream (downCov). A positive 5’-Cap sites had to meet the following criteria: (1) upFC = endCov/upCov≥2; (2) downFC = endCov/downCov≥2; (3) read counts≥10; (4) P-value<0.05; (5) existing in two replicates; (6) located within mRNA 5`UTR region.
Assembly: hg38, mm10
Supplementary files format and content: bigwig

source_name: Human hepatocellular carcinoma cells

value: non-treated

value: wild type


title: HepG2_RNAseq_rep1

description:
HepG2, non-treated, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: Cfpac1 cells, ChIPseq ELF3, Untreated, Rep1


title: HepG2_NAPseq_SHAPE-MaP_NAI-N3_rep3

description:
HepG2, NAI-N3-treated, biological replicate3
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: GCB_CK_rep5 [CKDKO_R5]

data_processing:
nfcore atac seq version 1.2.1
Assembly: mm10
Supplementary files format and content: Consensus Peak Counts

extract_protocol:
60,000 freshly sorted live cells were washed in cold PBS, lysed in 60 ul cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) for 3 min on ice, followed by addition of 1 ml wash buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20) and centrifugation to pellet nuclei.
Bulk ATAC-seq libraries were prepared following the Omni-ATAC protocol. Briefly, nuclei were resuspended in a transposition reaction mix prepared using the Illumina Tagment DNA Enzyme and Buffer Kit (Illumina, 20034197) and incubated at 37 ºC for 30 minutes on thermomixer at 1,000 rpm to allow for transposition-based DNA fragmentation and adapter ligation. Tagged DNA fragments were purified using the Clean & Concentrator-5 Kit (ZYMO, D4014), then subjected to PCR amplification and double-sided bead purification (to remove primer dimers and larger than 1,000 bp fragments) using the AMPure XP beads (Beckman Coulter, A63881).

treatment_protocol: Mice (WT, C, K, and CK) were immunized with SRBC for 10 days before sorting GC B cells.

value: GCB cell


title: DIPG066_T

description: Sample 92


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 48h, Rep3

value: Trametinib 48h


title: DIPG064_T

description: Sample 91


title: ARID1A_CnR_CSTantibody_WT2

description:
CnR_lib2
AvgWT_CST_cnr.bw


title: GCB_CK_rep4 [CKDKO_R4]


title: DIPG062_T

description: Sample 89


title: HepG2_NAPseq_SHAPE-MaP_NAI-N3_rep1

description:
HepG2, NAI-N3-treated, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: DIPG063_T

description: Sample 90


title: ED200211_t

description: total RNA

value: Forebrain

value: FACSorted for GFP


title: HepG2_NAPseq_SHAPE-MaP_DMSO_rep3

description:
HepG2, DMSO-treated, biological replicate3
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome

value: DMSO-treated


title: GCB_CK_rep2 [CKDKO_R2]


title: GCB_CK_rep1 [CKDKO_R1]


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 48h, Rep1


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 24h, Rep2

value: Trametinib 24h


title: HepG2_NAPseq_SHAPE-MaP_DMSO_rep1

description:
HepG2, DMSO-treated, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: HepG2_NAPseq_SHAPE-MaP_DMSO_rep2

description:
HepG2, DMSO-treated, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: GCB_K_rep3 [KKO_R3]


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 24h, Rep3


title: HepG2_NAPseq_SHAPE-MaP_NAI-N3_rep2

description:
HepG2, NAI-N3-treated, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 24h, Rep1


title: DIPG060_T

description: Sample 87


title: GCB_K_rep4 [KKO_R4]


title: DIPG058_T

description: Sample 86


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 48h, Rep2


title: DIPG061_T

description: Sample 88


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 12h, Rep3

value: Trametinib 12h


title: GCB_CK_rep3 [CKDKO_R3]


title: GCB_K_rep2 [KKO_R2]


title: HepG2_CAPseq_rep3

description:
HepG2, CAPseq, non-treated, biological replicate3
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: DIPG052_T

description: Sample 84


title: HepG2_CAPseq_rep1

description:
HepG2, CAPseq, non-treated, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 12h, Rep2


title: GCB_K_rep1 [KKO_R1]


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 12h, Rep1


title: DIPG030_T

description: Sample 83


title: HepG2_CAPseq_rep2

description:
HepG2, CAPseq, non-treated, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: GCB_C_rep4 [CKO_R4]


title: DIPG057_T

description: Sample 85


title: DIPG029_T

description: Sample 82


title: HepG2, poly(I:C)-treated, biological replicate3

description: Discover the full-length non-capped RNAs of the mammalian transcriptome

value: total RNA, remove rRNA


title: DIPG028_T

description: Sample 81


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 3h, Rep3

value: Trametinib 3h


title: HepG2, poly(I:C)-treated, biological replicate2


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 3h, Rep2

value: Wild type


title: GCB_C_rep1 [CKO_R1]


title: GCB_C_rep2 [CKO_R2]


title: GCB_C_rep3 [CKO_R3]


title: HepG2, CoCl2-treated, biological replicate2


title: Cfpac1 cells, ChIPseq H3K9me3, Untreated, Rep3


title: Cfpac1 cells, ChIPseq H3K9me3, Trametinib 3h, Rep1


title: HepG2, poly(I:C)-treated, biological replicate1


title: HepG2, CoCl2-treated, biological replicate1


title: GCB_WT_rep3 [WT_R3]


title: DIPG027_T

description: Sample 80

value: HGG


title: Cfpac1 cells, ChIPseq H3K9me3, Untreated, Rep2


title: DIPG026_T

description: Sample 79


title: GCB_WT_rep4 [WT_R4]

value: spleen


title: DIPG025_T

description: Sample 78


title: GCB_WT_rep2 [WT_R2]


title: DIPG019_T

description: Sample 77


title: Cfpac1 cells, ChIPseq H3K9me3, Untreated, Rep1

value: PDAC Low-Grade


title: HepG2, Adriamycin (ADR)-treated, biological replicate3

value: Adriamycin-treated


title: DIPG018_T

description: Sample 76


title: DIPG014_AUT

description: Sample 75


title: GCB_WT_rep1 [WT_R1]

value: WT


title: Panc1 cells, ChIPseq H3K27ac, Trametinib 24h, Rep2

value: PDAC High-Grade


title: HepG2, Adriamycin (ADR)-treated, biological replicate1

value: wild type


title: Panc1 cells, ChIPseq H3K27ac, Trametinib 24h, Rep1


title: GCB_BCK_rep4

description:
D235_CKDHET_R4
ck_bcl2_gcb_featurecounts.merged.counts.tsv

data_processing:
nfcore RNA version 2.0
Assembly: mm10 and hg38
Supplementary files format and content: Combined gene count table

growth_protocol: Human OCI-Ly7 cell lines were cultured in IMDM supplemented with 15% FBS, 1% L-Glutamine and 1% penicillin-streptomycin.

extract_protocol:
Total RNAs were extracted from sorted mouse cell suspensions using TRIzol LS Reagent (Invitrogen) or from human OCI-Ly7 cells using Rneasy mini plus kit (Qiagen) following the manufacturer’s instructions.
Libraries were made using the Illumina TruSeq stranded mRNA kit.

treatment_protocol: Mice (WT, C, K, and CK) were immunized with SRBC for 10 days before collecting CBs and CCs. Mice (BCL2, BCL2+C, BCL2+K, BCL+CK) were immunized with SRBC once every 3 weeks (starting at 56 days post-BMT) to induce continuous GC formation and lymphomagenesis, GC B cells were sorted at day 235 post BMT.

value: GCB cell


title: GCB_BCK_rep3

description:
D235_CKDHET_R3
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: Panc1 cells, ChIPseq H3K27ac, Trametinib 12h, Rep1


title: HepG2, non-treated, biological replicate3

value: non-treated


title: Panc1 cells, ChIPseq H3K27ac, Trametinib 12h, Rep2


title: GCB_BCK_rep2

description:
D235_CKDHET_R2
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: HepG2, non-treated, biological replicate2


title: DIPG007_T

description: Sample 73

data_processing: All data analysis used Bioconductor version 3.14 or 3.16 packages in R version 4.1 or 4.2, respectively, unless otherwise stated. Raw NanoString data (RCC files) was processed using the NanoStringQCPro package (v1.26.0). For quality control, the geometric mean of the housekeeping genes was used as a metric of overall RNA quality and quantity, and samples with a value of < 100 were excluded. The data from all samples was normalized together using housekeeping genes and positive control genes as recommended in the NanoString data analysis guidelines. Briefly, for each sample a normalization was performed sequentially using first the positive controls and then the housekeeping genes. For each sample the geometric mean of the positive controls was calculated (geomeancontrol). The geometric mean of all the geometric means was then calculated (geomeangeomeans) and this was used to calculate a sample specific normalization factor (geomeangeomeans /geomeancontrol), which was multiplied by the gene counts for each sample. The same steps were then taken using the housekeeping genes instead of the positive controls, to provide the final normalized gene counts.


title: HEK293T, biological replicate2

source_name: Human embryonic kidney 293T cells


title: DIPG006_T

description: Sample 72


title: HepG2, Adriamycin (ADR)-treated, biological replicate2


title: HEK293T, biological replicate3


title: Panc1 cells, ChIPseq H3K27ac, Trametinib 3h, Rep2


title: Panc1 cells, ChIPseq H3K27ac, Trametinib 3h, Rep1


title: DIPG005_T

description: Sample 71


title: GCB_BK_rep4

description:
D235_KHET_R4
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: GCB_BCK_rep1

description:
D235_CKDHET_R1
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: DIPG004_T

description: Sample 70


title: U87, biological replicate3

source_name: Uppsala 87 Malignant Glioma cells


title: Panc1 cells, ChIPseq H3K27ac, Untreated, Rep2

value: Untreated


title: GCB_BK_rep3

description:
D235_KHET_R3
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: AY01196

description: Sample 67

source_name: pediatric brain tumor

value: LGG


title: HEK293T, biological replicate1


title: DIPG003_T

description: Sample 69


title: Panc1 cells, ChIPseq H3K27ac, Untreated, Rep1


title: GCB_BK_rep2

description:
D235_KHET_R2
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: GCB_BC_rep4

description:
D235_CHET_R4
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: HepG2, non-treated, biological replicate1


title: U87, biological replicate2


title: DIPG008_T

description: Sample 74


title: MiaPaca2 cells, ChIPseq H3K27ac, Trametinib 24h, Rep2


title: MiaPaca2 cells, ChIPseq H3K27ac, Trametinib 24h, Rep1


title: MiaPaca2 cells, ChIPseq H3K27ac, Trametinib 12h, Rep2


title: AY01197

description: Sample 68


title: GCB_BC_rep3

description:
D235_CHET_R3
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: C2C12_D0_NAPseq_nanopore_rep3

description:
C2C12, 0 hours after differentiation, nanopore, biological replicate3
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome

source_name: mouse myoblast cells

value: 0 hours after differentiation


title: U87, biological replicate1


title: AY01056

description: Sample 65


title: AY01061

description: Sample 66


title: MiaPaca2 cells, ChIPseq H3K27ac, Trametinib 3h, Rep2


title: GCB_BC_rep2

description:
D235_CHET_R2
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: AY01054

description: Sample 64


title: MiaPaca2 cells, ChIPseq H3K27ac, Trametinib 12h, Rep1


title: C2C12_D0_NAPseq_nanopore_rep1

description:
C2C12, 0 hours after differentiation, nanopore, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: AY01048

description: Sample 63


title: MiaPaca2 cells, ChIPseq H3K27ac, Trametinib 3h, Rep1


title: GCB_BK_rep1

description:
D235_KHET_R1
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: Z138 # 7

city: Madison

first: Lixin

last: Rui

state: WI - Wisconsin

address: 1111 Highland Ave R.4060

department: Medicine

institute: University of Wisconsin-Madison

description: Genrich-KOasCtrl-DNMT3A-WT-Z138.bam.narrowPeak

data_processing:
Raw reads were mapped to the human reference genome (hg38) by by HISAT2 (v2.1), and differential expression analysis was done by StringTie (v1.3.4) and DESeq2 (Cite cite).  Differential expression analysis compares the changes of DNMT3A KO relative to control cells. Gene set enrichment analysis (GSEA) was performed by GSEA software (V4.0.1). For GSEA analysis, a pre-ranked gene list was generated using the formula rank = -log10(p)*(foldchange). The molecular signatures databases including h.all.v5.2 symbols, along with mitochondria -related gene sets were used.
For ChIP-seq analysis, raw reads were mapped to the human reference genome (hg38) by HISAT2 (V2.1) using default parameters. Identical reads were collapsed into one. Because all sequencing has high GC bias, including input controls, all datasets were corrected for GC bias using deepTools with computeGCbias and correctGCbias (Ramirez et al., 2016). ChIP-seq data were visualized in an Integrative Genomic Viewer (V2.3 40). Peaks were called by Genrich (V1.0) using default parameters. The MEME suite (with ±1 kb around a peak summit) was used for motif discovery (meme-suite.org). ChIPseeker was used to annotate and visual the distribution of peaks. EnrichedHeatmap (Bioconductor V1.14.0) was use for visualization of differential peak.
Assembly: hg38

extract_protocol:
Total RNA was extracted using TriZol according to the manufacturer’s protocol
ChIP: 10 ng of ChIP’ed DNA was used to generate the ChIP-seq library using Ovation Ultralow Library System V2 (NuGen Technologies), according to the manufacturer’s protocol
mRNA:  RNA-seq libraries were prepared by using the Illumina TruSeq stranded mRNA LT sample preparation kit (Illumina).

value: MCL

value: sgDNMT3A KO

value: doxycycline (2ng/mL)

tag: time

value: 7 days


title: AY01047

description: Sample 62


title: MiaPaca2 cells, ChIPseq H3K27ac, Untreated, Rep2

value: Wild type


title: Z138 WT

source_name: Z138 WT

value: Z138 WT


title: GCB_B_rep3

description:
D235_WT_R3
ck_bcl2_gcb_featurecounts.merged.counts.tsv

value: spleen


title: MiaPaca2 cells, ChIPseq H3K27ac, Untreated, Rep1


title: AY01045

description: Sample 61


title: Z138  # 7-DNMT3A KO-day 7-3


title: C2C12_D0_NAPseq_nanopore_rep2

description:
C2C12, 0 hours after differentiation, nanopore, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: GCB_B_rep2

description:
D235_WT_R2
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: Z138  # 7-DNMT3A KO-day 7-2


title: AY01042

description: Sample 60

value: HGG


title: GCB_B_rep1

description:
D235_WT_R1
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: Z138  # 7-DNMT3A KO-day 7-1


title: ADAR1-CD

city: Beijing

first: Zeliang

address: No.38 Xueyuan Road,Haidian

institute: Peking University Health Science Center

data_processing:
Adapter sequences and low quality reads were trimmed from both ends of the raw data using fastp software.
The clean reads were mapped to the VSV-GFP reference genome (https://www.ncbi.nlm.nih.gov/nuccore/FJ478454) and hg38 reference genome using Hisat2 (http://daehwankimlab.github.io/hisat2/, v2.2.1), respectively.
samtools (v1.3.1) and MySQL database were used to obtain the editing sites information.
Visualization of the distribution of editing sites in hg38 genome was performed with circus (v0.69-8).
Visualization of editing sites distribution along VSV genomic regions was performed with the Integrative Genomics Viewer (IGV, v2.9.4)
Assembly: Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP, complete genome (FJ478454.1); hg38
Supplementary files format and content: tab-delimited text files including count values for each sample

extract_protocol:
RNA was purified using Trizol reagent and rRNA was depleted according to stardard protocols
The library was constructed by Berry Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA).

treatment_protocol: Cells were treated with VSV-GFP for 6h

value: Human embryonic kidney

value: VSV-GFP infection


title: Z138  # 7-DNMT3A KO-day 5-3

value: 5 days


title: PTENα-N(6R/D)-ADAR1-CD


title: CC_CK_rep3

description:
CK.CC_R4
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: GCB_B_rep4

description:
D235_WT_R4
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: AY01036

description: Sample 59


title: PTENα-N(WT)-ADAR1-CD


title: Z138  # 7-DNMT3A KO-day 5-2


title: CC_CK_rep2

description:
CK.CC_R3
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: GCB_BC_rep1

description:
D235_CHET_R1
ck_bcl2_gcb_featurecounts.merged.counts.tsv


title: H3K4me3_CK_rep2

data_processing:
nfcore cutandrun version 2.0
DIffBind 3.6.1
ROSE
Assembly: hg38
Supplementary files format and content: DiffBind objects by mark (normalized to read depth)
Supplementary files format and content: DESeq2 combined objects by mark normalized to read depth at promoters
Supplementary files format and content: ROSE super enhancer calls based on WT H3K27Ac

source_name: GCB-DLBCL

extract_protocol:
Cells were immobilized to ConA beads and then subject to permeabilization, antibody binding, pAG-Mnase binding and activation, targeted chromatin digestion and release, and DNA recovery by NEB Monarch DNA Cleanup Kit according to the EpiCypher CUT&RUN Protocol.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) following the manufacture’s protocol.

value: GCB-DLBCL

value: Ab:EpiCypher 13-0028


title: AY01034

description: Sample 57

extract_protocol: Total RNA was extracted from FFPE and snap frozen tissue using RNAstorm FFPE and fresh frozen kits, respectively, as per the manufacturer's instructions (CellData). RNA concentration was measured (Nanodrop) and RNA integrity assessed using the Agilent 2100 bioanalyzer.


title: CC_CK_rep1

description:
CK.CC_R2
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv

value: GCB cell


title: AY01033

description: Sample 56


title: H3K4me3_CK_rep1


title: Z138  # 7-DNMT3A KO-day 5-1


title: CC_K_rep4

description:
K.CC_R4
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY01031

description: Sample 55


title: H3K4me3_K_rep2


title: Z138  # 7-control-3

value: uninduced


title: CC_K_rep3

description:
K.CC_R3
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY01035

description: Sample 58

value: LGG


title: H3K4me3_K_rep1


title: Z138  # 7-control-2


title: Z138  # 7-control-1


title: H3K4me3_C_rep2


title: CC_K_rep1

description:
K.CC_R1
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY01026

description: Sample 53


title: H3K4me3_C_rep1


title: CC_C_rep4

description:
C.CC_R4
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY01022

description: Sample 51


title: CC_C_rep3

description:
C.CC_R3
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: H3K4me3_WT_rep1

value: WT


title: AY01017

description: Sample 50


title: CC_C_rep2

description:
C.CC_R2
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: H3K27ac_CK_rep2

value: Ab:EpiCypher 13-0045


title: AY01015

description: Sample 49


title: CC_C_rep1

description:
C.CC_R1
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY01028

description: Sample 54


title: H3K27ac_CK_rep1


title: C3H10T1/2 cells, Osteogenesis,Day0

city: Nanjing

first: Wang

last: Bin

state: Jiangsu

address: No.305Zhongshan East Rd

institute: Jinling hospital, Medical School of Nanjing University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: HISAT2 v2.0.5
Supplementary files format and content: Excel file include FPKM values for each Sample

extract_protocol:
1. RNA degradation and contamination was monitored on 1% agarose gels; 2. RNA purity was checked using the NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA); 3. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H - ). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Mesenchymal stem cells

value: Osteogenesis differention


title: Input of E14.5 GE

data_processing:
61 bp single-end reads were trimmed using Cutadapt (v1.16) and mapped to mm10 using Bowtie2 (v2.3.0) followed by peak calling with MACS2 (v2.1.2) using a cutoff of q=0.01
Assembly: mm10-2.1.0
Supplementary files format and content: bigWig, narrowPeak (except for Input sample) from MACS2 output

source_name: Ganglionic Eminences

extract_protocol:
For ChIP-seq, ganglionic eminences and part of the underlying striatum of 70 embryos at E14.5 were microdissected and immediately fixed in 1% formaldehyde for 5 min. Samples were processed using the ChIP-IT High Sensitivity columns (Active Motif)
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). 3 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Ganglionic Eminences

value: Input


title: AY01013

description: Sample 47


title: CC_WT_rep4

description:
WT.CC_R4
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: CC_K_rep2

description:
K.CC_R2
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: H3K27ac_K_rep2


title: C3H10T1/2 cells, Osteogenesis,Day14


title: MEIS ChIP-seq of E14.5 GE

value: ChIP

value: anti-MEIS1a/2a, anti-MEIS2 (Mercader et al. (2005), Development)


title: CC_WT_rep3

description:
WT.CC_R3
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv

value: spleen


title: AY01023

description: Sample 52

value: HGG


title: H3K27ac_K_rep1


title: H3K4me3_WT_rep2


title: C3H10T1/2 cells, Osteogenesis,Day7


title: AY01006

description: Sample 45


title: C3H10T1/2 cells, Osteogenesis,Day1


title: H3K27ac_C_rep2


title: CC_WT_rep2

description:
WT.CC_R2
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY01007

description: Sample 46


description:
Cfpac1 cells, RNAseq Trametinib 24h, Rep2
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt

data_processing:
Fastq raw reads were processed with FASTQC tool v0.11.9 for quality base check and to exclude any technical bias in the data. Sequences were then checked for the presence of the adaptors using trimmomatic_v0.39. Trimmed single-end reads were then mapped onto the human genome GRCh38 assembly version using STAR-v.2.7.8a (PMID 23104886) with the following parameters: --limitSjdbInsertnsJ = 500,000, --alignIntronMax=1,000,000, --alignIntronMin=20. After uniquely mapped reads were retained, gene counts were retrieved using featureCounts on Gencode GRCh38 annotation (Ensembl 104 version). Next, protein-coding genes were selected and processed with the edgeR_3.39 R-package (PMID 19910308) for gene filtering, normalization and differential testing. Differentially expressed genes were defined using the following thresholds: absolute log Fold-Change value > 1 and FDR < 0.001.
Repetitive element analysis: RNAseq data were aligned onto the hg38 genome using STAR-v.2.7.8a with the following settings: --outFilterMultimapNmax 500 –winAnchorMultimapNmax 500. For the read count estimation, repeats were quantified using TEtranscript (PMID 26206304) in the ‘multi’ mode using the same gene annotation (GTF file) in primary RNA-seq analysis and a UCSC-RepeatMasker (v-4.1.1) GTF for the TE-annotation. Subfamily-level counts were processed with edgeR_v3.39 for data normalization and differential testing. Differentially-expressed subfamilies were defined by setting absolute log(Fold-Change) threshold of 1 and FDR < 0.05.
For the Cfpac1-ELF3KO data set, repetitive element analysis was performed using the same computational workflow described in the previous section.
Assembly: GRCh38 assembly version
Supplementary files format and content: tab-delimited files include gene-level normalized CPM values for each cell line.
Supplementary files format and content: tab-delimited files include CPM values of repeat subfamilies for each cell line.
Supplementary files format and content: Normalized coverage data are provided in BigWig format.

value: PDAC Low-grade

value: Wild type

value: Trametinib 24h


title: CC_WT_rep1

description:
WT.CC_R1
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: H3K27ac_C_rep1

value: GCB-DLBCL


title: AY01014

description: Sample 48


title: AY01000

description: Sample 43


title: AY01001

description: Sample 44


title: CB_CK_rep3

description:
CK.CB_R4
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv

value: GCB cell


title: H3K27ac_WT_rep2


description:
Cfpac1 cells, RNAseq Trametinib 12h, Rep3
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt

value: Trametinib 12h


title: AY00993

description: Sample 42

value: LGG


title: CB_CK_rep2

description:
CK.CB_R2
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: H3K27ac_WT_rep1

value: WT


title: CB_CK_rep1

description:
CK.CB_R1
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


description:
Cfpac1 cells, RNAseq Trametinib 12h, Rep2
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt


title: AY00992

description: Sample 41


description:
Cfpac1 cells, RNAseq Trametinib 24h, Rep3
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt


title: CB_K_rep3

description:
K.CB_R4
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


description:
Cfpac1 cells, RNAseq Trametinib 12h, Rep1
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt


title: H3K4me1_CK_rep2

value: Ab:EpiCypher 13-0040


title: AY00985

description: Sample 39


title: AY00986

description: Sample 40


title: H3K4me1_CK_rep1


description:
Cfpac1 cells, RNAseq Trametinib 3h, Rep3
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt

value: Trametinib 3h


description:
Cfpac1 cells, RNAseq Trametinib 3h, Rep2
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt


title: H3K4me1_K_rep2


description:
Cfpac1 cells, RNAseq Trametinib 24h, Rep1
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt


title: CB_K_rep2

description:
K.CB_R3
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: CB_K_rep1

description:
K.CB_R1
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: H3K4me1_K_rep1


description:
Cfpac1 cells, RNAseq Trametinib 3h, Rep1
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt


title: H3K4me1_C_rep2


title: AY00982

description: Sample 38


title: CB_C_rep3

description:
C.CB_R3
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: Cfpac1 cells, RNAseq Untreated, Rep3

description:
Cfpac1 cells, RNAseq Untreated, Rep3
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt

value: Untreated


title: AY00981

description: Sample 37


title: CB_C_rep4

description:
C.CB_R4
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY00978

description: Sample 36


title: H3K4me1_C_rep1


title: CB_C_rep2

description:
C.CB_R2
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: Cfpac1 cells, RNAseq Untreated, Rep2

description:
Cfpac1 cells, RNAseq Untreated, Rep2
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt


title: H3K4me1_WT_rep2


title: Cfpac1 cells, RNAseq Untreated, Rep1

description:
Cfpac1 cells, RNAseq Untreated, Rep1
Pdac.CFPAC1.genes.normalizedCounts.txt
Pdac.CFPAC1.repElements.normalizedCounts.txt


title: AY00977

description: Sample 35


title: CB_C_rep1

description:
C.CB_R1
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY00976

description: Sample 34


description:
Capan2 cells, RNAseq Trametinib 24h, Rep3
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


title: H3K4me1_WT_rep1


title: CB_WT_rep4

description:
WT.CB_R4
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: AY00975

description: Sample 33


title: OCI-Ly7_CK_rep2

description:
CREBBP_KMT2D_R2
ly7_featurecounts.merged.counts.tsv


title: CB_WT_rep3

description:
WT.CB_R3
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: CB_WT_rep2

description:
WT.CB_R2
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: OCI-Ly7_CK_rep1

description:
CREBBP_KMT2D_R1
ly7_featurecounts.merged.counts.tsv


title: AY00969

description: Sample 32


description:
Capan2 cells, RNAseq Trametinib 24h, Rep1
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


description:
Capan2 cells, RNAseq Trametinib 12h, Rep3
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


title: CB_WT_rep1

description:
WT.CB_R1
ck_sorted_gcb_rna_featurecounts.merged.counts.tsv


title: OCI-Ly7_K_rep2

description:
KMT2D_R2
ly7_featurecounts.merged.counts.tsv


title: OCI-Ly7_K_rep1

description:
KMT2D_R1
ly7_featurecounts.merged.counts.tsv


title: AY00968

description: Sample 31


title: AY00963

description: Sample 29


description:
Capan2 cells, RNAseq Trametinib 12h, Rep2
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


title: AY00961

description: Sample 28


title: OCI-Ly7_C_rep2

description:
CREBBP_R2
ly7_featurecounts.merged.counts.tsv


title: MEFs,Ptenα-/-,VSV 8h,rep 2

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: mouse embryonic fibroblast cells

extract_protocol:
RNA was purified using Trizol reagent and the integrity was assessed by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
The trancriptome libraries were prepared using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) and sequenced by the Illumina NovaSeq 6000

treatment_protocol: Cells were treated with VSV for eight hours

value: mouse embryonic fibroblast cells

value: Pten{alpha} KO

tag: infection

value: VSV


title: MEFs,Ptenα-/-,VSV 8h,rep 1


title: OCI-Ly7_C_rep1

description:
CREBBP_R1
ly7_featurecounts.merged.counts.tsv


title: MEFs,WT,VSV 8h,rep 2


description:
Capan2 cells, RNAseq Trametinib 3h, Rep3
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


description:
Capan2 cells, RNAseq Trametinib 12h, Rep1
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


title: OCI-Ly7_WT_rep2

description:
WT_R2
ly7_featurecounts.merged.counts.tsv


description:
Capan2 cells, RNAseq Trametinib 3h, Rep2
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


description:
Capan2 cells, RNAseq Trametinib 24h, Rep2
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


title: AY00958

description: Sample 26


title: AY00957

description: Sample 25


title: AY00967

description: Sample 30


title: PTIR1

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 3.2.3) was used for generation of Seurat object.
Low-quality cells with over 15% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 3.2.3). Top 40 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 3.2.3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: murine tumor infiltration lymphocytes

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
10x scRNA-Seq

value: BALB/c

value: tumor


description:
Capan2 cells, RNAseq Trametinib 3h, Rep1
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt

extract_protocol:
Total RNA from was extracted using the Quick-RNA Miniprep Kit (Zymo Research, R1055)
RNA-seq was carried out using the SMART-seq2 protocol (PMID 24385147) with minor modifications, as described (PMID 35568393)
Single-end and Paired-end RNAseq


title: Capan2 cells, RNAseq Untreated, Rep3

description:
Capan2 cells, RNAseq Untreated, Rep3
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt


title: Mock

value: mock


title: PTENα_Input RIP-seq

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018) software.
The clean reads were mapped to the VSV-GFP reference sequence (https://www.ncbi.nlm.nih.gov/nuccore/FJ478454) and hg38 using Hisat2 (http://daehwankimlab.github.io/hisat2/, v2.2.1) respectively.
A step-wise mapping procedure was applied: (1) Reads that not aligned to the VSV-GFP reference sequence or human genome sequence were discarded. (2) Reads with low alignment quality were removed. (3) Reads that aligned to the mitochondrial sequence were discarded. Peaks were identified using CHIPseeker.
Visualization of peak distribution along genomic regions of interested genes was performed with the Integrative Genomics Viewer (IGV).
Assembly: Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP, complete genome (FJ478454.1);hg38
Supplementary files format and content: BigWig

treatment_protocol: Cells were treated with VSV-GFP for 14h and irradiated with 400mJ/cm2 energy of 254 nm UV light

value: Human embryonic kidney

value: VSV-GFP infection


title: AY00953

description: Sample 24


title: OCI-Ly7_WT_rep1

description:
WT_R1
ly7_featurecounts.merged.counts.tsv


title: AY00950

description: Sample 23


title: PTENα

first: Yizhe

last: Sun

state: Beijing

address: No.38, Xueyuan Road ,Haidian District

description: 10x scRNA-Seq

data_processing:
The Cell ranger software pipeline (version 5.0.0) provided by 10x Genomics was used to demultiplex cellular barcodes, map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 3.2.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 3000 or less than 300, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 3.2.3). Top 40 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 3.2.3).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: features.tsv: gene files; barcodes.tsv: cell barcode files; matrix.mtx: gene-barcode counts.

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

tag: strain/background

value: B16 Pten-/- tumor

value: tumor infiltrating lymphocytes

value: PTEN-alpha expression


title: HuR [K120/182R] Input rep3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Human hepatoma HuH-7 cell line stably expressing HuR(K120/182R) SUMOylation mutant.
Stranded Total RNA-seq

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) software was used to generate gene counts.
Genome_build: human genome hg19
Supplementary_files_format_and_content: Text files containing gene counts.

source_name: cultured hepatoma cells

growth_protocol: Human hepatoma HuH-7 cells were grown in the medium stated in the manufacturer’s instructions. All cell lines were maintained in culture for a maximum of 20 passages in a humidified incubator at 37ºC and 5% CO2.

extract_protocol:
RNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol and precipitated overnight in the presence of 100% ethanol, sodium acetate 3 M pH 5.5 and GlycoBlue Coprecipitant. The RNA pellet was washed with 70% ethanol, air dried and resuspended in H2O.
The quantity and quality of the RNAs were evaluated using Agilent RNA 6000 Pico Chips (5067-1513, Agilent Technologies). 16-77 ng of RNA from each RIP sample and 250 ng of RNA from each input sample was used for RNA-seq library preparation. Sequencing libraries were prepared using the TruSeq Stranded Total RNA Human/Mouse/Rat kit (RS-122-2201, Illumina Inc.), following the manufacturer’s guidelines.

value: HuR [K120/182R] mutant expression


title: Capan2 cells, RNAseq Untreated, Rep1

description:
Capan2 cells, RNAseq Untreated, Rep1
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt

value: PDAC Low-grade

value: Wild type


title: PTENα_IP RIP-seq


title: HuR [K120/182R] Input rep2


title: AY00948

description: Sample 22

value: HGG


title: Mock

description: 10x scRNA-Seq

value: Mock


title: AY00960

description: Sample 27


title: Cfpac1 cells, ChIPseq H3K27ac, Trametinib 24h, Rep2

value: PDAC Low-Grade

value: Trametinib 24h


title: Capan2 cells, RNAseq Untreated, Rep2

description:
Capan2 cells, RNAseq Untreated, Rep2
Pdac.CAPAN2.genes.normalizedCounts.txt
Pdac.CAPAN2.repElements.normalizedCounts.txt

value: Untreated


title: MEFs,WT,VSV 8h,rep 1

value: mouse embryonic fibroblast cells

value: WT

value: VSV


title: HuR [K120/182R] Input rep1


title: Cfpac1 cells, ChIPseq H3K27ac, Trametinib 24h, Rep1


title: C2C12_D144_RNAseq_rep3

description:
C2C12, 144 hours after differentiation, biological replicate3
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome

extract_protocol:
RNA was harvested using Trizol reagent. 2ug total RNA was used to prepare the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina or nanopore protocols

value: 144 hours after differentiation

value: wild type


title: AY00947

description: Sample 21


title: WT-HuR Input rep3

description:
Human hepatoma HuH-7 cell line stably overexpressing WT HuR.
Stranded Total RNA-seq

value: HuR wild type overexpression


title: Cfpac1 cells, ChIPseq H3K27ac, Trametinib 12h, Rep2

value: Trametinib 12h


title: C2C12_D144_RNAseq_rep1

description:
C2C12, 144 hours after differentiation, biological replicate1
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: C2C12_D144_RNAseq_rep2

description:
C2C12, 144 hours after differentiation, biological replicate2
total RNA, remove rRNA
Discover the full-length non-capped RNAs of the mammalian transcriptome


title: AY00946

description: Sample 20

value: LGG