title: sperm_F1-13_Ldlrc1

first: Yuta

last: Takahashi

address: 10010 N Tottey Pines Rd

institute: Salk Institute

description: mouse with Ldlr CGI methylation

data_processing:
Bisulfite sequencing reads were checked for read quality using FastQC
aligned to the mm10 genome with Bismark (PMID: 21493656)
Bismark uses a C to T converted version of the genome and Bowtie (PMID: 19261174) alignment (we allowed maximum 1 seed mismatch) to identify base-specific methylation percentages.
Assembly: mm10
Supplementary files format and content: bedgraph

growth_protocol: Mice were bred in the animal facility of the Salk Institute

extract_protocol:
Genomic DNA was isolated from mice tails, sperms or ESCs using a proteinase K digestion-phenol/chloroform extraction based method.
Target enrichment-genome methyl sequencing was performed as described previously using the SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies) with a customized capture library following manufacturer's protocol. The biotinylated RNA capture probe library to capture specific genomic loci was designed to include three loci on mouse genome; mm10, chr6:118556982-118565982, chr9:111265293-111280293, and chr9:21720056-21729056. Three μg of genomic DNA was sheared to 150-180 bp fragments using Covaris M220. Following hybridization between sheared DNA and the capture library, captured genome DNA was purified using streptavidin beads. Bisulfite conversion of the captured DNA was performed using the EZ DNA Methylation-Gold Kit (Zymo Research). Following indexing and sample pooling with 10% PhiX, sequencing was conducted using Illumina NextSeq500, at PE150.
Target enriichment-genome bisulfite sequencing analysis

value: sperm

value: Ldlr c1 line

tag: targeted cgi

value: Ldlr CGI


title: WT mESC

status: Public on Feb 07 2023

type: SRA

city: La Jolla

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: WT mESC

tag: cell type

value: ES cell

tag: strain


title: RNAseq, ganglion_neurons_IL17A_96h, rep1

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

description: RNAseq_counts_dorsal_ganglion_neurons.txt

library_source: transcriptomic

data_processing:
RNA-seq samples were mapped to the mm10 mouse genome with STAR. Gene expression was assessed using HOMER’s analyze Repeats with parameters rna, mm10, -count exons, -condenseGenes. Raw data are shown as transcripts per million (TPM). Differential expression was calculated using DESeq2. Genes were considered differentially expressed with FDR < 0.05 and FC > 2. Gene ontology analysis was done with Metascape or IPA (Qiagen).
Genome_build: mm10
Supplementary_files_format_and_content: TPMs

molecule: total RNA

source_name: dorsal root ganglion neurons exposed to IL17-A in vitro for 96 hours

extract_protocol:
For S. aureus RNA-seq: Ear pinna skin was split into the dorsal and the ventral sheets and placed in RPMI 1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1 mM non-essential amino acids, 50 μM β-mercaptoethanol, 20 mM HEPES, 100 U/ml of penicillin, 100 mg/ml of streptomycin, 0.5 mg/ml of DNAse I (Sigma-Aldrich) and 0.25 mg/ml of Liberase TL purified enzyme blend (Roche) for 90 minutes at 37C and 5% CO2. Digested ear skin sheets were homogenized using the Medicon/Medimachine tissue homogenizer system. T cells were FACsorted (BD FACS Aria, Becton Dickinson) from Foxp3-GFP reporter mice. The RNA from the sorted T cells was extracted using the RNeasy Plus Micro Kit (Qiagen) as per manufacturer instructions. Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.
For DRG RNA-seq: Supernatant was removed from cells, cells were lysed with RLT Plus buffer (Qiagen) and the RNA was extracted to perform bulk RNA sequencing. Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.
Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.

treatment_protocol:
For S. aureus treatment: Staphyloccocus aureus (42F02) was cultured in tryptic soy broth for 4 hours at 37oC with shaking at 200 rpm. For commensal colonization, each mouse was topically associated by applying up to 5 mL of a culture of S. aureus (approximately 10^9 CFU/mL) across the entire skin surface, or by applying 1 mL in each ear skin, using a sterile cotton swab. Unless otherwise noted, associations were repeated every other day for a total of 4 times. For infections, mice were intradermally injected in the ear pinnae with 2x10^7 CFU of S. aureus (42F02).
For dorsal ganglion neuron treatment: 5000 cells were seeded into flat-bottom 96-well plates coated with laminin (Thermo Fisher) and allowed to attach to the bottom of the wells for 2 hours, then the medium was removed and replaced with neurobasal medium containing 50 ng/ul nerve growth factor (Thermo Fisher). Following an overnight incubation, the supernatant was removed and replaced with neurobasal medium containing 50 ng/ul nerve growth factor, 10 uM cytosine arabinoside (Sigma), and 100 ng/ml IL17-A. Culture medium was replaced daily for the duration of the experiment.

tag: treatment

value: dorsal ganglion neurons


title: scRNAseq_SSCR_D18_3

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

country: China

institute: Peking University

data_processing:
Library strategy: modified STRT-seq
For scRNA-seq data, We firstly extracted cell barcodes and UMI sequences from read 2 of raw fastq data by UMItools (v1.0.0) (Smith et al., 2017) and attached them after the read name of read 1. After TSO and polyA sequences removal by local scripts, the “clean” reads were aligned to the mouse mm10 reference genome using STAR (2.7.2b) (Dobin et al., 2013), gene features were assigned by featureCounts (v2.0.0) (Liao et al., 2014). We used UMItools to generate UMI count expression matrix. For the quality control of scRNA-seq data, cells with detected gene numbers fewer than 2,000 or the fraction of mitochondrial reads more than 5% were excluded from further analysis, besides, genes expressed in fewer than 3 cells were filtered out for analysis.
For bisulfite sequencing data, trim_galore (v0.6.4) were used to remove low quality reads and adaptor sequence, and 9 bp of random primers from 5’ end of both read 1 and read 2 were also trimmed. Clean reads were then mapped to mm10 genome using Bismark (v0.23.0) with paired-end mode and ‘--non_directional’ option. Unmapped reads were outputted and mapped again by single-end mode. Aligned bam files were merged and sorted by samtools (v 1.11) and PCR duplicates were marked by picard MarkDuplicates (v2.23.6). Methylation calls for each CpG site were extracted by ‘bismark_methylation_extractor’ of Bismark. The thresholds for CpG sites coverage were 1X and 3X for single-cell- and bulk DNA methylation, respectively. Only methylation levels less than 10% or greater than 90% were retained for single-cell methylation data. Bisulfite conversion rate (BSCR) was estimated by methylation ratio of lambda DNA, samples with BSCR greater than 98% and detected CpG sites greater than 1,000,000 were kept for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix: matrix of UMI counts for all genes in each cell
Supplementary_files_format_and_content: bismark coverage: genome-wide cytosine report outputs of Bismark methylation extractor

molecule: polyA RNA

source_name: Cells induced from SSC

growth_protocol: SSCs were cultured in StemPro-34 SFM (Gibico, USA) supplemented with 20 ng/ml EGF, 10 ng/ml bFGF, 10 ng/ml GDNFand 1000 U/ml ESGRO. gPSC were cultured in N2B27 medium supplemented with 2iL.

extract_protocol:
For modified STRT-seq and scTrio-seq2, RNA and DNA are extracted with lysis buffer.  For PBAT and WGBS, genomic DNA was extracted using FastPure Cell/Tissue DNA Isolation Mini Kit.
The libraries for modified STRT-seq, Trio-seq2, PBAT and WGBS are performed according to the previously reported studies (Dong et al., 2018) (Bian et al., 2018) (Smallwood et al., 2014) (Li et al., 2010)

treatment_protocol: The reprogramming process is induced with- or without five mechanicals in 24-well culture plates.

value: C57BL/6[female] X DBA[male]


title: LdlrHR1ex

description: mouse with Ldlr CGI methylation


title: scRNAseq_SSCR_D18_4


title: F1-4_Ankrd SL c1

description: mouse with Ankrd26 CGI methylation Seamless

source_name: F1-4_Ankrd SL c1

value: Tail

value: Ankrd SL c1  line

value: Ankrd26 CGI


title: Ankrd SL c1

source_name: Ankrd SL c1


title: USB1 mut D16, 2

city: boulder

first: Roy

last: parker

address: colorado ave

institute: university of colorado boulder

data_processing:
Adapters were trimmed and reads shorter than 19nt were dropped using Cutadapt 2.5
Trimmed reads were aligned to human mature miRNA release from miRbase 22 using Bowtie2 2.2.9
Aligned reads were co-ordinate shorted to BAM files using Samtools 1.3.1
miRNA counts were extracted from BAM files
Differential expression between WT and USB1 mutant miRome was calculated using DEseq2
Assembly: miRbase 22
Supplementary files format and content: CSV file containing counts of miRNA reads

organism: Homo sapiens

extract_protocol:
Cells were collected and lysed using Trizol
Lexogen Small RNA-seq library prep kit

tag: cell line

value: Human embryonic stem cells

tag: genotype

value: USB1 mut

value: Hematopoietic differentiation


title: sperm_Ankrd c3

description: mouse with Ankrd26 CGI methylation

source_name: sperm_Ankrd c3

value: Ankrd c3 line


title: scRNAseq_SSCR_D16_6


title: USB1 mut D16, 1


title: scRNAseq_SSCR_D16_5


title: RNAseq, ganglion_neurons_Control_96h, rep3

source_name: dorsal root ganglion neurons exposed to control in vitro for 96 hours

value: Control


title: RNAseq, ganglion_neurons_Control_96h, rep4


title: F2-8_F1-1x2_Ankrd c3

description: mouse with Ankrd26 CGI methylation


title: Control D16, 3

value: WT


title: RNAseq, ganglion_neurons_Control_96h, rep2


title: scRNAseq_SSCR_D16_4


title: Control D16, 2


title: HSPA5_1

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

data_processing:
Base-calling was done with bcl2fastq2 conversion software (NovaSeq 6000)
Read alignment and counting was done using Rsubread package (v. 2.0) using in-built RefSeq gene annotation.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file rsubread_featureCounts.csv is tab delimited text file containing the genewise read counts for each sample.

source_name: cell

growth_protocol: The HTR-8/Svneo cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 U/ml penicillin, 100 mg/ml streptomycin, 2 mM glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was isolated by using RNeasy Micro Kit
TruSeq® Stranded mRNA Sample Preparation, Illumina (15031047)

treatment_protocol: The transfection with siRNA was done either with 10 nM siRNA pair or 10 nM siRNA universal negative control and using approximately 100 000 cells and duoble transfection. The first transfection was done in suspension and the second transfection in adherent cells.

value: trophoblast

tag: tissue

value: placenta

value: silenced with siRNA of HSPA5


title: Ankrd c3

description: mouse with Ankrd26 CGI methylation

source_name: Ankrd c3


title: scRNAseq_SSCR_D16_3


title: scRNAseq_SSCR_D18_2


title: Control D16, 1


title: scRNAseq_SSCR_D18_1


title: Vero_m6A

city: Gothenburg

first: Tanmoy

last: Mondal

state: Västra Götaland

address: Bruna Stråket 16

department: Department of Clinical Chemistry and Transfusion Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
RIP-seq: Single-end sequencing reads from SMARTer-Stranded Total RNA-Seq Kit v2 were analyzed with FastQC for quality control (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), adapters were removed using Trim Galore v0.6.6 with a minimal length threshold of 20bp. Trimmed reads were aligned to the concatenated chlSab2 (Chlorosebus sabeus), wuhCor1 (SARS-CoV-2) reference genomes obtained from the UCSC Genome Browser (http://hgdownload.soe.ucsc.edu/goldenPath/) and ecoli-k12 (Escherichia coli K-12 spike-in, substr. MG1655, U00096.2) from NCBI. Reads were mapped using HISAT2 v2.2.1 with parameters (-U --rna-strandness R). Duplicate alignments were labeled using markDuplicates from Picard v2.23.4 and further processed using Sambamba keeping uniquely mapping reads separated by strand after duplicate removal. The number spike-in reads were calculated by counting the reads uniquely mapping to the E. coli genome. Coverage tracks were generated normalizing for spike-in and input using deepTools. m6A peak calling on SARS-CoV-2 viral genome and infected cell samples was performed with callpeak from MACS2 v2.2.6 on IP and input processed alignments mapped to SARS-CoV-2 wuhCor1 reference genome or the concatenated genomes (chlSab2 + wuhCor1 + ecoli-k12) for infected and non-infected samples, using the parameters “--no-model --keep-dup auto --call-summits” and effective genome sizes of 3 x 104 bp and a p-value cutoff of 0.05 and 2.76 x 10^9 and a p-value cutoff of 0.01, respectively. Called peaks were annotated with annotatePeaks.pl from HOMER v4.11 using default parameters.
RAN-seq: Uniquely mapping reads were quantified using featureCounts from the Rsubread package, following by differential expression analysis with DESeq2. Genes were considered differentially expressed with an absolute log2 fold change value > 1 and an adjusted p-value of < 0.01.
Genome_build: Chlorocebus sabaeus: chlSab2
Genome_build: SARS-CoV-2: wuhCor1
Genome_build: Escherichia coli K-12, substr. MG1655: U00096.2
Supplementary_files_format_and_content: RNA-seq: featureCounts matrix
Supplementary_files_format_and_content: RIP-seq: bigwig files for coverage; narrowPeak files for called peaks

organism: Chlorocebus sabaeus

source_name: Vero cells

growth_protocol: Vero CCL-81 cells were cultured in DMEM, 1% penicillin-streptomycin and 10% fetal calf serum at 37°C at 5% CO2.

extract_protocol:
RNA was isolated from Vero CCL-81 cells (non-infected and post 48h infection) using TRIZOL reagent (Invitrogen). RNA fragmentation followed by m6A RIP was performed with 15ug of RNA spiked-in with 9 ng of Bacterial RNA.
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 (Pico Input Mammalian) from Takara and single-end sequenced (1X 88 bp) on Illumina NextSeq 2000 platform.

treatment_protocol: T25 flasks with Vero CCL-81 (ATCC) were infected with the three different SARS-CoV-2 variants and medium or infected cells were harvested in trizol post 48 hours infection for RNA-sequencing studies.

value: Vero CCL-81 cells

tag: antibody

value: m6A (Synaptic Systems, Cat# 202003)

value: Non-infected Vero cells

tag: spike-in organism

value: Escherichia coli K-12

tag: molecule subtype

value: m6a-modified RNA


title: RNAseq, ganglion_neurons_Control_96h, rep1

value: dorsal ganglion neurons


title: Vero_totalRNA_input_2


title: RNAseq, CCR6_pos_Saureus_TA, rep3

source_name: CCR6 positive (Tc17) T cells topically associated with S. aureus (TA)

value: topical association with S. aureus (TA)

value: ear skin

value: CCR6 positive (Tc17) T cells


title: USB1 mut D0, 2

value: Human embryonic stem cells

value: USB1 mut


title: Vero_input_1


title: RNAseq, CCR6_pos_Saureus_TA, rep2


title: USB1 mut D0, 3

value: Hematopoietic differentiation


title: scRNAseq_SSCR_D16_2

value: C57BL/6[female] X DBA[male]


title: F1-1_Ankrd c3

description: mouse with Ankrd26 CGI methylation

value: Tail

value: Ankrd c3 line

value: Ankrd26 CGI


title: scRNAseq_SSCR_D16_1


title: USB1 mut D0, 1


title: scRNAseq_SSCR_D14_5


title: Control D0, 3

value: WT


title: SARS-CoV-2_B.1..1.7_Infected_cell_input_1

value: Vero CCL-81 cells

value: SARS-CoV-2 B.1.1.7-infected Vero cells


title: RNAseq, CCR6_pos_Saureus_TA, rep1


title: scRNAseq_SSCR_D14_4


title: SARS-CoV-2_B.1..1.7_Infected_cell_totalRNA_input_2


title: Control D0, 2


title: RNAseq, CCR6_pos_Saureus_TA_ID, rep2

source_name: CCR6 positive (Tc17) T cells topically associated and then injected with S. aureus (TA + ID) (recall)

value: topical association and injection with S. aureus (TA + ID)


title: scRNAseq_SSCR_D14_3


title: RNAseq, CCR6_pos_Saureus_TA_ID, rep1


title: Control D0, 1


title: SARS-CoV-2_B.1.351_Infected_cell_m6A

value: m6A (Synaptic Systems, Cat# 202003)

value: SARS-CoV-2 B.1.351-infected Vero cells

value: Escherichia coli K-12


title: scRNAseq_SSCR_D14_2


title: RNAseq, CCR6_pos_Saureus_ID, rep2

source_name: CCR6 positive (Tc17) T cells injected with S. aureus (ID)

value: injection with S. aureus (ID)


title: USB1 KO 3


title: SARS-CoV-2_B.1.351_Infected_cell_input_1


title: scRNAseq_SSCR_D14_6


title: SARS-CoV-2_B.1..1.7_Infected_cell_m6A

value: m6a-modified RNA


title: SARS-CoV-2_B.1.351_Infected_cell_totalRNA_input_2


title: scRNAseq_SSCR_D14_1


title: RNAseq, CCR6_pos_Saureus_TA_ID, rep3

value: ear skin

value: CCR6 positive (Tc17) T cells


title: RNAseq, CCR6_pos_Saureus_ID, rep1


title: USB1 KO 1

value: USB1 mut


title: scRNAseq_SSCR_D12_3


title: USB1 KO 2


title: scRNAseq_SSCR_D12_2


title: RNAseq, CCR6_neg_Saureus_TA, rep2

source_name: CCR6 negative (Tc1) T cells topically associated with S. aureus (TA)

value: topical association with S. aureus (TA)

value: CCR6 negative (Tc1) T cells


title: SARS-CoV-2_B.1_Infected_cell_input_1

value: SARS-CoV-2 B.1-infected Vero cells


title: scRNAseq_SSCR_D12_1

value: C57BL/6[female] X DBA[male]


title: SARS-CoV-2_B.1_Infected_cell_totalRNA_input_2


title: Control 2


title: scRNAseq_SSCR_D10_1


title: RNAseq, CCR6_neg_Saureus_TA_ID, rep3

source_name: CCR6 negative (Tc1) T cells topically associated and then injected with S. aureus (TA + ID) (recall)


title: Control 1


title: 2FX1_sample3

type: genomic

city: Berlin

first: Arend

last: Koch

state: Berlin

address: Charitéplatz 1

department: Dept. of Neuropathology

country: Germany

institute: Charité Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip and Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
The IDAT.files were uploaded to the methylation classifier (brain tumor  classifier v11b4, Capper et al., 2018, Nature). The classifier generates a PDF showing the methylation class and the CNV profile (See https://www.molecularneuropathology.org/mnp/). Statistical analysis was done using the minfi package running on R version 3.6.1 (2019-07-05) -- "Action of the Toes".
Classification reports could not be provided because they contain patient information. However, "Methylation family class" and "Methylation subclass" are provided in the sample descriptions along with the respective Classifier Score values. This is the essential information that is generated in the PDF report from the uploaded IDATs. The procedure for uploading the IDATs to the Brain Tumor Classifier is described on the following website: https://www.molecularNeuropathology.org/  [Classifier Version v11b4]

label: Cy3, Cy5

source_name: Tumor

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted form FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) , according to the manufacturer’s instructions

tag: gender

value: f

tag: who diagnosis

value: Oligodendroglioma, IDH-mutant and 1p19q-codeleted grade 3

value: Tumor

tag: methylation family (class version v11b4)

value: methylation class family glioma, IDH mutant

tag: maximal calibrated family score

tag: methylation subclass (version v11b4)

value: 1p/19q codeleted oligodendroglioma

tag: maximal calibrated subclass score


title: RNAseq, CCR6_neg_Saureus_TA_ID, rep2

value: topical association and injection with S. aureus (TA + ID)


title: NASH Diet Pck1 Knockout Mice 5

city: chongqing

first: tang

last: ni

address: yixueyuan Road NO.1

institute: Chongqing Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: the livers of Pck1-cKO mice fed a NASH diet for 24 weeks

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diet

value: NASH diet for 24 weeks

value: liver

tag: age

value: 31-33 Weeks


title: RNAseq, CCR6_neg_Saureus_TA, rep3

tag: cell type


title: RNAseq, CCR6_neg_Saureus_TA_ID, rep1

tag: strain


title: sample30

value: m

value: high grade astrocytoma (v12b5:oligosarcoma)


title: MED411-3_S6

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: MED411-3, Pediatric brain tumor isolate, medulloblastoma (MED).

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and employed a single-end, 50 base read length (SE100) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg38 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw values for each sample.

extract_protocol:
Cells were lysed with Trizol (Thermo Fisher Scientific). Total RNA was then isolated using a Direct-zol RNA kit (Zymo Research) and quality validated on the Agilent 2200 TapeStation. RNA concentration was measured using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Pediatric Brain Tumor isolate


title: RNAseq, CCR6_neg_Saureus_ID, rep3

source_name: CCR6 negative (Tc1) T cells injected with S. aureus (ID)

tag: treatment

value: injection with S. aureus (ID)

value: ear skin


title: scRNAseq_SSCR_D0_1

source_name: Spermatogonial stem cell


title: sample25


title: SARS-CoV-2_B.1_Infected_cell_m6A

value: Vero CCL-81 cells

value: m6A (Synaptic Systems, Cat# 202003)

value: Escherichia coli K-12

value: m6a-modified RNA


title: sample27

value: Oligodendroglioma, IDH-mutant and 1p19q-codeleted grade 3


title: RNAseq, CCR6_neg_Saureus_TA, rep1

value: topical association with S. aureus (TA)

value: CCR6 negative (Tc1) T cells


title: DIPG4E-3_S3

description: DIPG4E-3 , Pediatric brain tumor isolate, diffuse intrinsic pontine glioma (DIPG)


title: MED411-2_S5

description: MED411-2 , Pediatric brain tumor isolate, medulloblastoma (MED).


title: Control 3

tag: cell line

value: WT


title: sample29

value: Tumor

value: methylation class family glioma, IDH mutant

value: 1p/19q codeleted oligodendroglioma


title: NASH Diet Pck1 Knockout Mice 3

value: NASH diet for 24 weeks

value: liver

tag: genotype

value: 31-33 Weeks


title: NASH Diet Pck1 Knockout Mice 2

tag: tissue


title: RNAseq, CCR6_neg_Saureus_ID, rep1


title: sample28

value: f


title: DIPG4E-2_S2

description: DIPG4E-2, Pediatric brain tumor isolate, diffuse intrinsic pontine glioma (DIPG)

value: Pediatric Brain Tumor isolate


title: Rpb1ChIP_dcp2_Replicate_3

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 6 Center Drive

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

institute: National Institutes of Health

data_processing:
For RNA-Seq: As described earlier (Martin-Marcos et al. 2017), Illumina sequencing reads were trimmed to remove the constant adapter sequence, mixed sample sequences were separated by the sample barcodes followed by removal of PCR duplicates using a custom Python (3.7) script. The sequences aligned to yeast non-coding RNAs were removed using bowtie (Langmead et al., 2009) and non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae genome (R64-1-1 S288C Saccer3 Genome Assembly) using TopHat (Trapnell et al., 2009). Only uniquely mapped reads from the final genomic alignment were used for subsequent analyses. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
For ChIP-Seq: Sequence data were aligned to the SacCer3 version of the genome sequence using Bowtie2 with parameters -X 1000 -very-sensitive, to map sequences up to 1 kb with maximum accuracy. PCR duplicates from ChIP-seq data were removed using the samtools rmdup package.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. Foe CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads. For Rpb1 ChIP-Seq, average occupancy  file contains five columns providing: systemmatic gene name (ORF), avg occupancy at -1, NDR, +1 and average of -1, NDR, +1

organism: Saccharomyces cerevisiae

source_name: Whole cells

extract_protocol:
Briefly, for ChIP assays, chromatin was prepared from formaldehyde-crosslinked cells, immunoprecipitated with Rpb1 antibodies, and the DNA was extracted . DNA libraries for Illumina paired-end sequencing were prepared using DNA Library Prep Kit for Illumina from New England Biolabs
In additional columns of the SAMPLES section
In additional columns of the SAMPLES section


title: sample26


title: Chow Diet Pck1 Knockout Mice 5

source_name: the livers of  Pck1-cKO mice fed a Chow diet for 24 weeks

value: Chow diet for 24 weeks


title: DIPG4E-1_S1

description: DIPG4E-1, Pediatric brain tumor isolate, diffuse intrinsic pontine glioma (DIPG)


title: Rpb1ChIP_dcp2_Replicate_2

growth_protocol: In additional columns of the SAMPLES section


title: ATRT-311-3_S15

description: ATRT-311-3 , Pediatric brain tumor isolate, atypical teratoid/rhabdoid tumors (ATRT)


title: NASH Diet Pck1 Knockout Mice 4


title: sample24

value: m


title: MED411-1_S4

description: MED411-1, Pediatric brain tumor isolate, medulloblastoma (MED).


title: sample23


title: Chow Diet Pck1 Knockout Mice 4


title: RNAseq, CCR6_neg_Saureus_ID, rep2

value: injection with S. aureus (ID)

value: ear skin


title: ATRT-311-2_S14

description: ATRT-311-2, Pediatric brain tumor isolate, atypical teratoid/rhabdoid tumors (ATRT)


title: Rpb1ChIP_WT_Replicate_3


title: Chow Diet Pck1 Knockout Mice 3


title: Rpb1ChIP_dcp2_Replicate_1


title: Rpb1ChIP_WT_Replicate_2


title: ATRT-311-1_S13

description: ATRT-311-1 , Pediatric brain tumor isolate, atypical teratoid/rhabdoid tumors (ATRT)


title: sample21


title: ATRT-310-3_S12

description: ATRT-310-3 , Pediatric brain tumor isolate, atypical teratoid/rhabdoid tumors (ATRT)


title: Rpb1ChIP_WT_Replicate_1


title: Chow Diet Pck1 Knockout Mice 2


title: Chow Diet Pck1 Knockout Mice 1


title: sample22


title: sample20

value: Astrocytoma, IDH-mutant grade 3

value: astrocytoma


title: NASH Diet Pck1 Knockout Mice 1


title: NASH Diet Pck1 Wild type Mice 5

source_name: the livers of WT mice fed a NASH diet for 24 weeks


title: ATRT-310-1_S10

description: ATRT-310-1 , Pediatric brain tumor isolate, atypical teratoid/rhabdoid tumors (ATRT)


title: ATRT-310-2_S11

description: ATRT-310-2 , Pediatric brain tumor isolate, atypical teratoid/rhabdoid tumors (ATRT)


title: sample19


title: RNA_edc3scd6_Replicate_2

extract_protocol:
For RNA-seq library preparation, total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using Zymo RNA Clean and Concentrator kit. and the library was prepared by NHLBI Sequencing and Genomics Core at NIH (Bethesda, MD) using TruSeq Stranded mRNA Library Prep Kit (Illumina)
In additional columns of the SAMPLES section
In additional columns of the SAMPLES section

value: W303 H5626 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 scd6delta-::HygMX4 edc3delta-::KanMX4)


title: Sample_827_FBX-2

description: FBXO42 ko  samples for GSC-0827

source_name: FBXO42 ko  samples for GSC-0827

value: Proneural GSC


title: sample18

value: Astrocytoma, IDH-mutant grade 4


title: NASH Diet Pck1 Wild type Mice 3

value: WT


title: Sample_827_FBX-1

description: FBXO42 ko  samples for GSC-0827


title: NASH Diet Pck1 Wild type Mice 2


title: sample16

value: Tumor

value: methylation class family glioma, IDH mutant


title: Sample_827_Ctrl-2

description: FBXO42 control samples for GSC-0827

source_name: FBXO42 control samples for GSC-0827


title: sample17

value: high grade astrocytoma


title: NASH Diet Pck1 Wild type Mice 1

value: NASH diet for 24 weeks

value: liver


title: Sample_827_Ctrl-1

description: FBXO42 control samples for GSC-0827


title: sample15

value: f


title: Hepatocyte, prep 3, metformin

city: Aurora

first: Stephanie

middle: R

last: Wesolowski

state: Colorado

address: MS F441

institute: Dr

data_processing:
gSNAP, Cufflinks, and R for sequence alignment and ascertainment of differential gene expression
differential expression analyzed with paired t-test
Assembly: Oar_v3.1
Supplementary files format and content: FPKM read counts

organism: Ovis aries

source_name: hepatocyte

extract_protocol:
RNA was isolated using Rneasy kit from Qiagen according to instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatocyte

value: metformin


title: Hepatocyte, prep 2, metformin


title: Hepatocyte, prep 4, metformin


title: Chow Diet Wild type Mice 5

source_name: the livers of WT mice fed a Chow diet for 24 weeks

value: Chow diet for 24 weeks

value: 31-33 Weeks


title: sample14

value: m


title: Chow Diet Wild type Mice 4


title: sample13

value: Astrocytoma, IDH-mutant grade 3


title: Hepatocyte, prep 4, basal

value: basal


title: Sample_660_FBX-2

description: FBXO42 ko samples for NSC-CB660

source_name: FBXO42 ko samples for NSC-CB660

value: NSC ISOLATE


title: Chow Diet Wild type Mice 3


title: Hepatocyte, prep 1, metformin


title: Hepatocyte, prep 3, basal


title: Sample_660_Ctrl-2

description: FBXO42 control samples for NSC-CB660

source_name: FBXO42 control samples for NSC-CB660


title: RNA_edc3scd6_Replicate_1

value: W303 H5626 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 scd6delta-::HygMX4 edc3delta-::KanMX4)


title: NASH Diet Pck1 Wild type Mice 4


title: Sample_660_FBX-1

description: FBXO42 ko samples for NSC-CB660


title: Hepatocyte, prep 2, basal


title: Chow Diet Wild type Mice 2


title: sample12

value: Astrocytoma, IDH-mutant grade 4

value: not classifiable


title: sample11

value: Tumor

value: astrocytoma


title: Sample_660_Ctrl-1

description: FBXO42 control samples for NSC-CB660


title: Hepatocyte, prep 1, basal


title: Chow Diet Wild type Mice 1

value: WT


title: ChOR_T0_ClickedInput_Ring1B_IAAdTAG_rep2

status: Public on Feb 06 2023

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description: EdU-labelled genomic DNA

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were read into Seqmonk (v1.47.1) with MAPQ>20, ignoring duplicates, and reads extended by 250bp. Samples were normalized based on Drosphila spike-In abundance and corresponding ClickedInputs. Replicates were merged, exported as bedgraphs and converted to bigwig using UCSC BedGraphtoBigWig
Assembly: mm10
Assembly: dm6
Assembly: hg38
Supplementary files format and content: bigwig files for merged replicates (RRPM-adjusted)  for the mouse genome. RPM for human genome
Library strategy: ChOR-seq

source_name: Embryonic stem cells

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE. HCT116 cells were grown at 37 °C with 5 % CO2. DMEM was supplied with 1x Glutamax (Gibco), 10% FBS and 1x penicillin/strep.

extract_protocol: After the appropriate treatment, cells were washed with cold PBS, crosslinked for 5min (RING1B: 10min) with 1% Formaldehyde at room temperature and subsequently quenched with 0.1M Glycin (final concentration) for 5min before harvesting. Then, nuclei were isolated and sonicated using the Covaris Chromatin Shearing Kit. ChIP-Immunoprecipation of chromatin was done using antibodies according to the manufacturers recommendation with EdU-labelled Drosophila S2 chromatin serving as Spike-In control and, where the epitope of the antibody does not recognize the Drosophila homolog (i.e. H2A.Z) , H2AV antibodies to immunoprecipitate Spike-In chromatin as well. Purified fragments were biotinylated, libraries prepared, EdU-biotinylated fragments pulled down using Streptavidin and sequenced

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min and then either collected (T0) or cultured for indicated maturation intervals (T15-T480, in minutes) in media without EdU before collection. If treated with DMSO (volume equivalent), Triptolide (10uM), Indole-3-acetic acid (500uM) and/or dTAG-13 (1uM), cells were incubated for indicated times in the description and then  collected.

value: Ring1AKO Ring1BmAID BAP1dTAG

value: Indole-3-acetic (IAA) 500uM, dTAG-13 (1uM) for 80min


title: ChOR_T120_ClickedInput_T2_Ring1B_DMSO_rep1

description: EdU-labelled genomic DNA


title: ChOR_T120_ClickedInput_T2_Ring1B_DMSO_rep2

description: EdU-labelled genomic DNA


title: ChOR_T120_Ring1B_DMSO_rep1

description:
EdU-labelled genomic DNA
ChOR_RRPM_T2_Ring1B_DMSO.bw


title: ChOR_T0_ClickedInput_Ring1B_DMSO_rep1

description: EdU-labelled genomic DNA


title: ChOR_T0_ClickedInput_Ring1B_IAAdTAG_rep1

description: EdU-labelled genomic DNA


title: ChOR_T0_Ring1B_IAAdTAG_rep2

description: EdU-labelled genomic DNA


title: ChOR_T0_Ring1B_DMSO_rep1

description:
EdU-labelled genomic DNA
ChOR_RRPM_T0_Ring1B_DMSO.bw


title: ChOR_T0_Ring1B_IAAdTAG_rep1

description:
EdU-labelled genomic DNA
ChOR_RRPM_T0_Ring1B_dTAGIAA.bw


title: ChOR_T0_ClickedInput_Ring1B_DMSO_rep2

description: EdU-labelled genomic DNA


title: ChIP_Input_Ring1B_DMSO_rep1

description: .bw file for all replicates is included on R1 sample.

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were read into Seqmonk (v1.47.1) with MAPQ>20, ignoring duplicates,  reads extended by 250bp and normalized to the number of million of reads (RPM). Replicates were merged, exported as bedgraph and converted to bigwig using UCSC BedGraphToBigWig
Broad Peaks were called on bam files with MACS2 (v2.2.6) using pooled Inputs as control with parameters --nomodel, FDR q=0.05, read extension 250bp, -b (broad option) with cutoff q=0.1
Peak sets of individual replicates were concatanated, sorted using BEDtools SortBED, overlapping and adjacent peaks (<500bp) merged using BEDtools Merge. From this resulting peakset only peaks were kept that overlap the peakset of individual replicates.
Assembly: mm10
Assembly: dm6
Assembly: hg38
Supplementary files format and content: bigwig files, bed files for called Peak regions for the mouse or human genome (in RRPM when appropriate)

extract_protocol: After the appropriate treatment, cells were washed with cold PBS, crosslinked for 5min (JARID2 and RING1B: 10min) with 1% Formaldehyde at room temperature and subsequently quenched with 0.1M Glycin (final concentration) for 5min before harvesting. Then, nuclei were isolated and sonicated using the Covaris Chromatin Shearing Kit. ChIP-Immunoprecipation of chromatin was done using antibodies according to the manufacturers recommendation. Libraries were prepared from purified fragments  and sequenced.

treatment_protocol: If cells were treated, they were incubated with DMSO (volume equivalent) or Triptolide (10uM) for indicated times in the description before collection.


title: ChOR_T0_Ring1B_DMSO_rep2

description: EdU-labelled genomic DNA


title: ChIP_Ring1B_IAAdTAG_rep1


title: ChIP_Ring1B_DMSO_rep1


title: ChIP_Ring1B_IAAdTAG_rep2


title: ChIP_Input_Ring1B_DMSO_rep2


title: ChIP_Ring1B_DMSO_rep2


title: ChIP_Input_Ring1B_dTAGIAA_rep2


title: ChIP_Input_Ring1B_dTAGIAA_rep1


title: ChOR_T0TPL_ClickedInput_HCT116_TPL_rep1

description: EdU-labelled genomic DNA

source_name: colon cancer HCT116 cells

value: wildtype

value: Triptolide (10uM) for 20min


title: ChOR_T0_ClickedInput_HCT116_DMSO_rep2

description: EdU-labelled genomic DNA


title: ChOR_T0TPL_ClickedInput_HCT116_TPL_rep2

description: EdU-labelled genomic DNA


title: ChOR_T0_ClickedInput_HCT116_DMSO_rep1

description: EdU-labelled genomic DNA


title: ChOR_T120_Ring1B_DMSO_rep2

description: EdU-labelled genomic DNA


title: 40 di-sq 1

type: RNA

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from APC 50% for 48 h

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on Clariom_S_Mouse Array. GeneChips were washed and stained in the GeneAtlas® Fluidics Station

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Genes with a linear fold change >1.5 and p-value < 0.05(one-way between-subjects ANOVA) were considered as differentially expressed genes(DEGs). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software.
algorithm: RMA

label: biotin

source_name: cell treated with 40uM di-sq

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: B16F10 cells were purchaced from RIKEN and were maintained in RPMI1640

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added to each sample well and then the total RNA sample in 70% ethanol was stored at -20oC until use.

treatment_protocol: After the 24 hour seeding  in 6-well plates.  The medium was changed with 0 (Control) and 2.5 µM with di-sq and 40µM di-sq  for 48 h.

value: murine melanoma cells

value: 40 µM di-sq


title: 40 di-sq 2


title: ChOR_T0_HCT116_H2AZ_DMSO_rep2

description: EdU-labelled genomic DNA


title: Control2

description: Gene expression data from meduim treated for 48 h

source_name: cell treated with meduim

value: control


title: Control1


title: 2.5 di-sq 2

source_name: cell treated with 2.5uM di-sq

value: 2.5 µM di-sq


title: ChOR_noEdU_HCT116_H2AZ_DMSO_rep2

description: noEdU-labelled (control) genomic DNA


title: 2.5 di-sq 1


title: ChOR_T0_HCT116_H2AZ_DMSO_rep1

description:
EdU-labelled genomic DNA
ChOR_T0_HCT116_H2AZ_DMSO.bw


title: ChOR_noEdU_HCT116_H2BK120ub1_rep2

description: noEdU-labelled (control) genomic DNA


title: ChOR_T0TPL_HCT116_H2BK120ub1_TPL_rep1

description:
EdU-labelled genomic DNA
ChOR_T0TPL_HCT116_H2BK120ub1_TPL.bw


title: ChOR_T0_HCT116_H2BK120ub1_DMSO_rep2

description: EdU-labelled genomic DNA


title: ChOR_T0TPL_HCT116_H2BK120ub1_TPL_rep2

description: EdU-labelled genomic DNA


title: ChOR_T0_HCT116_H2BK120ub1_DMSO_rep1

description:
EdU-labelled genomic DNA
ChOR_T0_HCT116_H2BK120ub1_DMSO.bw


title: ChIP_Input_HCT116_T0TPL_rep1


title: ChIP_HCT116_H2BK120ub1_T0TPL_rep2


title: ChIP_HCT116_H2BK120ub1_T0TPL_rep1


title: ChOR_noEdU_HCT116_H2BK120ub1_rep1

description: noEdU-labelled (control) genomic DNA


title: ChIP_HCT116_H2BK120ub1_T0_rep2


title: ChIP_HCT116_H2AZ_T0_rep2


title: ChIP_Input_HCT116_T0_rep2


title: ChIP_Input_HCT116_T0_rep1


title: ChIP_Input_HCT116_T0TPL_rep2


title: ChIP_HCT116_H2AZ_T0_rep1


title: ChIP_HCT116_H2BK120ub1_T0_rep1


title: siPP2A rep 1 (PP2A-A knockdown), BS-Seq

city: Tampere

first: Reetta

last: Nätkin

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology, Prostate Cancer Research Center

institute: Tampere University and Tays Cancer Center

data_processing:
Reads were trimmed with TrimGalore! v0.6.4_dev with the following parameters: --quality 22 -- phred33 --gzip --rrbs --fastqc --paired --cores 4
Resulting trimmed paired-end reads were aligned with Bismark v0.22.3 using the Bowtie2 aligner v2.3.5.1 and the following additional parameters: --unmapped -- ambiguous --ambig_bam --nucleotide_coverage --fastq. Data were aligned to the Ensembl Homo Sapiens GRCh38 v95 genome and corresponding annotations were used.
Methylation calls were extracted with the bismark_methylation_extractor and the following parameters: -- paired-end --comprehensive --gzip --bedGraph --remove_spaces --buffer_size 80% - -cytosine_report --ignore_r2 2.
Assembly: hg38
Supplementary files format and content: methylation information in bedGraph format generated with Bismark methylation extractor

source_name: Uterus; Cervix

growth_protocol: Supplemented DMEM.

extract_protocol:
DNA was isolated using the Qiagen AllPrep DNA/RNA/Protein Mini Kit.
According to Boyle, Clement et al. 2012.

treatment_protocol: Transfections were done utilizing RNAiMAX transfection reagent, according to manufacturers instructions.

value: Uterus; Cervix

value: HeLa

value: Epithelial cells

value: siRNA (PP2A) transfected sample


title: siPP2A rep 2 (PP2A-A knockdown), BS-Seq


title: siPP2A rep 3 (PP2A-A knockdown), BS-Seq


title: siCtrl rep 3 (Control knockdown), BS-Seq

value: siRNA (control) transfected sample


title: ChOR_noEdU_HCT116_H2AZ_DMSO_rep1

description: noEdU-labelled (control) genomic DNA


title: siCtrl rep 2 (Control knockdown), BS-Seq


title: treated with Formate for 24h -rep3

city: Esch-sur-Alzette

first: Rashi

last: Halder

address: 7, Avenue des Hauts-Fourneaux

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine

data_processing:
Illumina software bcl2fastq (v2.20.0.422) was used for fastq file generation
Triming and adapter removal (AdapterRemoval ver. 2.3.1)
alignment (STAR 2.7.4a, parameters : " --twopassMode Basic --outSAMtype BAM SortedByCoordinate --limitOutSJcollapsed 1000000 --limitSjdbInsertNsj 1000000 --outFilterMultimapNmax 100 --outFilterMismatchNmax 33 --outFilterMismatchNoverLmax 0.3 --seedSearchStartLmax 12 --alignSJoverhangMin 15 --alignEndsType Local --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0.3 --winAnchorMultimapNmax 50  --alignSJDBoverhangMin 3")
Genome_build: homo_sapiens GRCh38 release 100
Supplementary_files_format_and_content: tab delemited text file including count values for each samples generated using Rsubread v 2.2.2

source_name: LN299 cell line

growth_protocol: LN229 cells  were cultured in Dulbecco’s modified Eagle’s medium (DMEM) without glucose, glutamine and phenol red (Thermo Fisher Scientific: A1443001) supplemented with 17 mM glucose (Sigma: G8769), 2 mM glutamine (Sigma-Aldrich: 25030081) and 10% qualified south American fetal bovine serum (FBS) (Thermo Fisher Scientific: 10500064).

extract_protocol:
Total RNA was extracted directly from the cell culture dishes using Rneasy Mini Kit (Qiagen:74104). RNA integrity and quantity were determined using the Agilent 2100 Bioanalyzer according to the manufacturer's manual. A RNA Integrity Number (RIN) above 9 was accepted for downstream analysis.
TruSeq Stranded mRNA Library prep kit ()
Stranded mRNA

treatment_protocol: The cells were treated for 0h, 8h, or 24 hours with 500 uM Na-Formate.

value: treated with formate


title: treated with Formate for 8h -rep3


title: siCtrl rep 1 (Control knockdown), BS-Seq


title: treated with Formate for 8h -rep2


title: siPP2A (PP2A-A knockdown)

data_processing:
Reads were aligned on the human genome GRCh38 with Bowtie2 v2.3.4.1, converted to bam with samtools v1.8, sorted with Picard SortSam v2.27.1
Bam files were indexed with Picard BuildBamIndex v2.27.1 and duplicated reads were marked with Picard MarkDuplicates v2.27.1
Peaks were called with MACS2 v2.1.0 with the following parameters: --gsize hs –qvalue 0.05 – format bam –nomodel –bdg –call-summits
Assembly: hg38
Supplementary files format and content: locations of statistically significantly enriched genomic regions detected by MACS2 tool in NARROWPEAK format

extract_protocol:
DNA was purified accroding to Buenrostro, Wu et al., 2015, using Qiagen MinElute PCR Purification Kit.
According to Buenrostro, Wu et al., 2015, using Illumina kit.


title: treated with Formate for 8h -rep1


title: siCtrl (Control knockdown)


title: treated with Formate for 24h -rep2


title: Control at 0 timepoint - rep1

value: untreated


title: Control at 0 timepoint - rep3


title: treated with Formate for 24h -rep1


title: Control at 0 timepoint - rep2


title: MFA129 D3 WT IP batch 3 [498_lib_08928AAB_CAGATC]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: WT IP

data_processing:
Reads were aligned against UCSC mm10 rRNA genome genome to identify rRNA contaminated reads with Bowtie1 1.2.3 and options -n2 -m1.
non-rRNA reads were aligned against the mm10 genome with Bowtie 2 2.2.2 and options -q -N1.
3'UTR coordinates for the mm10 genome were obtained from Ensembl Biomart (March 2017). 3'UTR counts were generated with R 3.5.1 and featureCounts from RSubread v1.32.4 with options allowMultiOverlap=TRUE,countMultiMappingReads=FALSE,minMQS=1 over mm10 3'UTR regions.
Reads from technical replicates (sequencing batches) were added before performing downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: Excel XLSX

source_name: Activated CD8 T cells

growth_protocol: Spleen and lymph nodes from WT and Cpeb4 KO animals were mechanically processed into single cell suspension. CD8 T cells were purified using Dynabeads™ FlowComp™ Mouse CD8 Kit (ThemoFisher). T cells were cultured in RPMI medium (Gibco) supplemented with 10% Fetal Bovine Serum, 1% penicillin/streptomycin, 2mM L-glutamine (Gibco), 1mM sodium pyruvate (Gibco) and 55 μM β-mercaptoethanol at 37ºC, 5% CO2 and 5% O2.

extract_protocol:
RNA was extracted by phenol-chlorofom following manufacturers instructions.
a single mRNA-purification step from 0.8 µg of RNA was applied to input samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and no purification steps was done on the IP samples. NGS libraries for RNA-seq were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). Twelve and seven cycles of PCR amplification were applied to input and IP libraries, respectively

treatment_protocol: Purified T cells were activated for 48h with 1 μg/ml anti-CD3 antibody (clone 145-2C11, MA5-17655, ThermoFisher), 1 μg/ml anti-CD28 antibody (clone CD28.6, 16-0288-85, eBiosciences) and 20 ng/ml IL-2 (212-12, Peprotech)

value: CD8 T cells

tag: rip antibody

value: anti-CPEB4 (homemade)


title: MFA129 D3 KO IP batch 2 [499_04945AAB_CTTGTA]

description: KO IP


title: MFA129 D3 KO Input batch 2 [497_04943AAB_GCCAAT]

description: KO Input


title: MFA129 D3 WT IP batch 2 [498_04944AAB_CAGATC]

description: WT IP


title: RIP8 KO Input batch 1 [1801_2019_02828AAA_GATCAG]

description: KO Input


title: MFA129 D3 WT Input batch 2 [496_04942AAB_ACAGTG]

description: WT Input


title: RIP8 KO IP batch 1 [1803_2019_02830AAA_GGCTAC]

description: KO IP


title: RIP8 KO IP batch 2 [1803_04937AAB_GGCTAC]

description: KO IP


title: RIP8 WT IP batch 2 [1802_04936AAB_TAGCTT]

description: WT IP


title: RIP8 KO Input batch 2 [1801_04935AAB_GATCAG]

description: KO Input


title: RIP8 WT input batch 1 [1800_2019_02827AAA_ACTTGA]

description: WT input


title: MFA129 D1 KO IP batch 3 [114_lib_08927AAB_TGACCA]

description: KO IP


title: MFA129 D1 KO IP batch 2 [114_04941AAB_TGACCA]

description: KO IP


title: RIP8 WT input batch 2 [1800_04934AAB_ACTTGA]

description: WT input


title: MFA129 D1 WT IP batch 3 [113_lib_08926AAB_TTAGGC]

description: WT IP


title: MFA129 D1 WT IP batch 2 [113_04940AAB_TTAGGC]

description: WT IP


title: MFA129 D3 KO IP batch 3 [499_lib_08929AAB_CTTGTA]

description: KO IP


title: MFA129 D1 WT Input batch 2 [111_04938AAB_ATCACG]

description: WT Input


title: MFA129 D1 KO Input batch 2 [112_04939AAB_CGATGT]

description: KO Input


title: MFA111 3039 R [1179_34488_TAGCTT]

data_processing:
FastQ files were aligned with STAR 2.7.0a against the mm10 genome using default options.
Gene level counts (Ensembl Biomart Mus musculus annotation, date 20190916) were generated using the featureCounts function from the Rsubread package 1.32.4 and default options.
Genome_build: mm10
Supplementary_files_format_and_content: Gene level counts

source_name: CD8 T lymphocytes

extract_protocol:
RNA was extracted by phenol-chlorofom following manufacturers instructions.
RNA depletion treatment were applied to the Input samples using (NEBNext rRNA depletion kit catalog number# E6310) following the manufacturer's intructions. Library generation were performed with  NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following manufacturer´s instructions and 9 cycles of amplification.

value: CD8 T lymphocytes

value: WT

tag: Sex

value: female

tag: timepoint

value: R


title: MFA111 3027 R [1179_34488_TGACCA]

value: KO


title: MFA111 3041 R [1179_34488_GTGAAA]


title: MFA111 3025 48H [1179_34488_CGATGT]


title: MFA111 3038 R [1179_34488_CAGATC]


title: MFA111 3041 48H [1179_34488_GAGTGG]


title: MFA111 3040 48H [1179_34488_CCGTCC]


title: RIP8 WT IP batch 1 [1802_2019_02829AAA_TAGCTT]

description: WT IP


title: MFA111 3040 R [1179_34488_ATGTCA]


title: MFA111 3025 R [1179_34488_ATCACG]


title: MFA111 3038 48H [1179_34488_ACTTGA]


title: MFA111 3027 48H [1179_34488_ACAGTG]


title: siRNA_2

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

data_processing:
The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI-Shenzhen, China).
FAStQC software was used to QC the raw data obtained from sequencing, and then Q30 values and GC content of sequencing data were calculated.
Read count extraction and normalization were performed using pig genomic benchwork
Hisat software was selected to perform genome alignment on clean reads, and it was found that the valid reads (90.55%-91.20%) could be aligned to the reference genome, indicating good sequencing results.
Supplementary files format and content: The excel table contains the FPKM value and read count for each example

organism: Sus scrofa

source_name: adipogenic differentiation

growth_protocol: The growth medium (GM) contained Dulbecco’s modified Eagle medium (DMEM, Gibco, Carlsbad, CA, USA) and 20% fetal bovine serum (FBS, Gibco).

extract_protocol:
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase Hor Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA.
Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control.

treatment_protocol:
After the growth of porcine primary preadipocytes, the cells were digested with trypsin to 80% density for passaging or inoculation of cell plates.
After the cells proliferated to the appropriate density in the cell culture plate, the cells were treated with insulin (Sigma, USA), 3-isobutyl 1-methylxanthine (IBMX, Sigma, USA), and dexamethasone (DEX, Sigma, USA) to induce cell differentiation

value: adipocytes

value: Primary adipocyte

value: inhibition

value: Day 8


title: Sample 1_HeLa_Ctrl_1st

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa_control plasmid

growth_protocol: he human HeLa cell line was obtained from the Institute of Biochemistry and Cell Biology (Chinese Academy of Sciences, Shanghai, China). HeLa cells were cultured with 5% CO2 at 37 °C in DMEM (Dulbecco’s modified Eagle’s medium), which were with 10% FBS (fetal bovine serum), 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: The transfection of HeLa cells with a FDPS-overexpressing plasmid was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer s instructions.

value: HeLa

tag: genotype/variation

value: control plasmid


title: Sample 3_HeLa_FDPS_1st

source_name: HeLa_FDPS overexpression

value: FDPS overexpression


title: Sample 2_HeLa_Ctrl_2nd


title: OElncRNA_3

value: Overexpression


title: Sample 4_HeLa_FDPS_2nd


title: siRNA_1


title: X. laevis male processed 7/23/19

city: Pittsburgh

first: Joel

middle: C

last: Rosenbaum

state: PA

address: 4249 5th Ave

institute: University of Pittsburgh

description: Mid output 150

data_processing:
Base calling performed by Phred
Sequencing reads uploaded to usegalaxycom
Alignments against X. laevis genome (V10.1) using HISAT2 with defaults for paired reads
Aligned fragments mapped and quantified with featurecounts using Xenbase (V10.1) as reference
Assembly: Xenbase genome (V10.1)

organism: Xenopus laevis

source_name: testis

growth_protocol: Lab strains grown under normal conditions.

extract_protocol:
Qiashredder and RNeasy
Illumina TruSeq mRNA kit with AMPure XP cleanup

treatment_protocol: Untreated.

value: testis

value: mixed testis

value: outcross


title: OElncRNA_1


title: X. laevis male processed 8/19/19

description: Mid output 150

value: untreated


title: OElncRNA_2


title: control_1


title: control_2


title: DIV5, UNC1999, rep2

city: New York

first: Kärt

last: Mätlik

state: NY

address: 1230 York Ave

institute: Rockefeller University

description:
DIV5_UNC1999_rep2
RNAseq_counts.csv

data_processing:
Reads were mapped to mm10 using Rsubread (version 1.30.6) (Liao et al., 2019)
Transcript abundance was calculated using Salmon (version 0.8.2) (Patro et al., 2017)
Counts were retrieved using Tximport (version 1.8.0) (Love et al., 2016)
Normalized, fragment extended signal bigWigs were created using rtracklayer (version 1.40.6) (Lawrence et al., 2009)
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes transcript counts for each sample
Supplementary files format and content: bigWig

source_name: cerebellum

growth_protocol: For preparing GC cultures, primary GCs were isolated from the cerebella of P6-P7 C57Bl/6J mice as described in (Hatten, 1985). Aliquots of freshly isolated GCPs were set aside for the DIV0 time point.

extract_protocol:
RNA from cultured GCs was isolated using RNeasy Micro Kit (Qiagen) with on-column DNA digestion. TRAP RNA was isolated as in (Heiman et al., 2008 and Doyle et al., 2008). Briefly, homogenized GCPs isolated from P7 Tg(Atoh1-Egfp-L10a) mice and cerebellar lysates from P7, P12 and P21 Tg(NeuroD1-Egfp-L10a) mice were incubated with Streptavidin MyOne T1 Dynabeads conjugated with anti-GFP monoclonal antibodies (Memorial Sloan-Kettering Monoclonal Antibody Facility) overnight at 4°C. The beads were then washed with 0.35 mM KCl TRAP Wash Buffer and resuspended in 100 µl RLT Buffer from the RNeasy Micro Kit supplemented with 1% β-mercaptoethanol. The resuspended beads were incubated at RT for 10 min, placed on a magnet, and the supernatant containing the RNA was collected and purified using the RNeasy Micro Kit. RNA integrity was determined using Bioanalyzer RNA 6000 Pico kit (Agilent) prior to library preparation.
RNAseq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina in conjunction with the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina. Libraries were sequenced at the Rockefeller University Genomics Resource Center using a NextSeq 500 sequencer to obtain 75-bp single-end reads.

treatment_protocol: Granule cells were cultured in the presence of DMSO or 100 nM UNC1999 and isolated on days 2 and 5 in vitro (DIV).

value: cerebellum

value: cultured primary granule cells

tag: developmental stage

tag: time


title: siRNA_3


title: DIV5, DMSO, rep1

description:
DIV5_DMSO_rep1
RNAseq_counts.csv

value: DMSO


title: DIV2, DMSO, rep1

description:
DIV2_DMSO_rep1
RNAseq_counts.csv


title: DIV2, DMSO, rep2

description:
DIV2_DMSO_rep2
RNAseq_counts.csv


title: X. laevis male processed 11/8/19

description: Mid output 150


title: DIV5, DMSO, rep2

description:
DIV5_DMSO_rep2
RNAseq_counts.csv


title: DIV5, UNC1999, rep1

description:
DIV5_UNC1999_rep1
RNAseq_counts.csv


title: Pool3, MC38, CD45+

city: Boston

first: Nicolas

middle: Alejandro

last: Gort-Freitas

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description: Contains libraries Tumor_CD45pos_Trx_E, Tumor_CD45pos_Trx_G

library_source: transcriptomic single cell

data_processing:
Sequencing and basecalling was carried out on NextSeq_2_1_0.
Fastq files were generated from Illumina base calls through bcl2fastq with the following flags/parameters: —adapter-stringency 0.9 --barcode-mismatches 0 --fastq-compression-level 4 --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --min-log-level INFO --minimum-trimmed-read-length 0 --processing-threads 8 --no-lane-splitting --mask-short-adapter-reads 0 --use-bases-mask y*,y*,y*,y*()
Processing of fastq files leading to pre-filtered count matrices (including alignment, genome mapping) was performed through STAR-solo
Single cell data filtering and normalization: We applied count filters on total and mitochondrial counts in order to retain high quality transcriptomes. We manually determined library-specific thresholds on total counts (ranging from 120 to 400 counts) and fraction of counts coming from mitochondrial genes (ranging from 12% to 15%) based on the empirical distributions of these magnitudes in each library. Subsequently, expression matrices were normalized to 10,000 counts per cell.
Dimensionality reduction and visualization of single cell data: To attain a low dimensional embedding of the transcriptomes, we first determined a set of highly variable genes based on the corrected Fano Factor (V-statistic) as defined in Klein et al. (2015) (Klein et al., 2015). We then performed PCA on the expression matrix resulting from retaining only highly-variable genes (160 components), computed a kNN graph (k=10), and obtained a UMAP 2D embedding of the pooled libraries.
Cell multiplet removal: We employed Scrublet (Wolock et al., 2019) to remove transcriptomes derived from two or more cells entering the same microfluidic droplet. We considered the cells with the top 1.9% doublet scores assigned by Scrublet as putative multiplets and verified that they co-localized in the UMAP embedding. This threshold was suggested by the software based on the distribution of doublet scores.
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: Raw counts (tsv.gz): library identity, barcode, and raw counts for all cells included in each pool
Supplementary files format and content: Library barcodes: library identity, barcode for all cells across all pools

source_name: MC38 murine colon carcinoma

growth_protocol: IL-12p40-IRES-EYFP (Jackson Labs Cat #006412) mice were injected in the flank with MC38 tumor cells, which were allowed to grow for 7 days.

extract_protocol:
Two days after the anti-CD40 treatment time point, mice were sacrificed and livers and tumors were isolated for generating single cell suspensions. Tissues were enzymatically digested, passed through a cell strainer, and cells were stained for CD45 and labeled with 7AAD; CD45+ cells were sorted using a BD FACSAria sorter. InDrops single cell RNA sequencing was performed.
A microfluidic device was used to co-encapsulate individual cells and polyacrylamide beads carrying barcoding reverse transcription (RT) primers and lysis reagents into 2-3 nl droplets, followed by primer release and RT at 50°C. After the RT reaction, droplets were broken, and the resulting barcoded cDNA was taken through the following sequencing library preparation steps 1) second strand synthesis, 2) in vitro transcription providing linear amplification of the material, 3) fragmentation of the amplified RNA, 4) a second reverse transcription using random hexamer primers bearing a universal PCR primer annealing site, and 5) indexing PCR, yielding a sequencing-ready library.

treatment_protocol: Tumor-bearing mice were injected intraperitoneally with 5 mg / kg agonist anti-CD40 monoclonal antibody, or left untreated

value: MC38 murine colon carcinoma

tag: tag

value: IL-12p40-IRES-EYFP transgene


title: Pool1, MC38, CD45+

description: Contains libraries Tumor_CD45pos_NT_A, Tumor_CD45pos_NT_B, Tumor_CD45pos_Trx_A, Tumor_CD45pos_Trx_B

value: Untreated, aCD40


title: Pool2, MC38, CD45+

description: Contains libraries Tumor_CD45pos_NT_C, Tumor_CD45pos_NT_D, Tumor_CD45pos_Trx_C, Tumor_CD45pos_Trx_D


title: Pool4, MC38, CD45+

description: Contains libraries Tumor_CD45pos_Trx_F, Tumor_CD45pos_Trx_H


title: MFA111 3039 48H [1179_34488_GGCTAC]

value: CD8 T lymphocytes

value: WT

value: female


title: P7 TRAP input

description:
P7_TRAP_input
RNAseq_counts.csv

value: total cerebellum


title: P21 Neurod1-bacTRAP, rep5

description:
P21_Neurod1_TRAP_rep5
RNAseq_counts.csv

value: granule cells

tag: molecule subtype

value: TRAP RNA


title: P12 TRAP input

description:
P12_TRAP_input
RNAseq_counts.csv


title: control_3

value: adipocytes

value: Primary adipocyte

value: Day 8


title: P12 Neurod1-bacTRAP, rep5

description:
P12_Neurod1_TRAP_rep5
RNAseq_counts.csv


title: P21 Neurod1-bacTRAP, rep1

description:
P21_Neurod1_TRAP_rep1
RNAseq_counts.csv


title: P21 Neurod1-bacTRAP, rep3

description:
P21_Neurod1_TRAP_rep3
RNAseq_counts.csv


title: P12 Neurod1-bacTRAP, rep4

description:
P12_Neurod1_TRAP_rep4
RNAseq_counts.csv


title: P12 Neurod1-bacTRAP, rep3

description:
P12_Neurod1_TRAP_rep3
RNAseq_counts.csv


title: P12 Neurod1-bacTRAP, rep1

description:
P12_Neurod1_TRAP_rep1
RNAseq_counts.csv


title: DIV0, rep1

description:
DIV0_rep1
RNAseq_counts.csv


title: DIV0, rep2

description:
DIV0_rep2
RNAseq_counts.csv


title: P7 Neurod1-bacTRAP, rep5

description:
P7_Neurod1_TRAP_rep5
RNAseq_counts.csv


title: P7 Neurod1-bacTRAP, rep3

description:
P7_Neurod1_TRAP_rep3
RNAseq_counts.csv


title: P21 TRAP input

description:
P21_TRAP_input
RNAseq_counts.csv


title: P7 Neurod1-bacTRAP, rep2

description:
P7_Neurod1_TRAP_rep2
RNAseq_counts.csv


title: P7 Math1-bacTRAP, rep2

description:
P7_Math1_TRAP_rep2
RNAseq_counts.csv


title: P21 Neurod1-bacTRAP, rep4

description:
P21_Neurod1_TRAP_rep4
RNAseq_counts.csv


title: P7 Math1-bacTRAP, rep4

description:
P7_Math1_TRAP_rep4
RNAseq_counts.csv


title: P21 Neurod1-bacTRAP, rep2

description:
P21_Neurod1_TRAP_rep2
RNAseq_counts.csv


title: P7 Math1-bacTRAP, rep3

description:
P7_Math1_TRAP_rep3
RNAseq_counts.csv


title: P12 Neurod1-bacTRAP, rep2

description:
P12_Neurod1_TRAP_rep2
RNAseq_counts.csv


title: P7 Math1-bacTRAP, rep1

description:
P7_Math1_TRAP_rep1
RNAseq_counts.csv


title: P21, Input for P21 H3K27me3 rep4

data_processing:
ChIP-seq reads were mapped using Rsubread (version 1.30.6) (Liao et al., 2019)
Peak calls were made with HOMER (version 4.11, style histone, size=1000, minDist=2500) (Heinz et al., 2010)
Peaks were annotated and genome distribution was determined using ChIPseeker (version 1.30.3) (Yu et al., 2015)
Normalized, fragment extended signal bigWig files were created using rtracklayer (version 1.40.6) (Lawrence et al., 2009)
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes counts at TSS ± 500 bp for each IP sample
Supplementary files format and content: bigWig, bed

extract_protocol:
P7 granule cell progenitors (GCPs) were isolated from the cerebella of C57Bl/6J mice using Percoll gradient sedimentation as described in (Hatten, 1985) and fixed with 1% formaldehyde for 7 min at room temperature. GC nuclei from P12 and P21 cerebella from C57Bl/6J mice were isolated using fluorescence-activated nuclei sorting as described in (Xu et al., 2018), using 1% formaldehyde (7 min) for fixation. Anti-NeuN (Millipore #MAB377) and anti-NeuroD (Santa Cruz Biotechnology #sc-1084) primary antibodies were used to label GC nuclei. Labeled NeuN+/NeuroD1+ nuclei were sorted using a BD FACSAria cell sorter. Cells and nuclei were lysed, and chromatin was sonicated using a Covaris E220 focused ultrasonicator in an AFA Fiber Pre-Slit Snap-Cap microTUBE at 140W peak power, 10% duty factor, and 200 cycles/burst for 1 min 50 s (P7 GCP nuclei) or 2 min 10 s (P12 and P21 GC nuclei). Triton X-100 was added at a final concentration of 1% and insoluble chromatin was pelleted by centrifugation. 5 % of chromatin was used for input.
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina) or the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The quality of the sequencing libraries was evaluated using the Agilent 2200 TapeStation with D1000 High Sensitivity ScreenTape. Libraries were sequenced at the Rockefeller University Genomics Resource Center using a NextSeq 500 sequencer to obtain 75-bp single-end reads.

tag: chip antibody


title: P21, Input for P21 H3K27me3 rep3


title: P12, Input for P12 H3K27me3 rep1 and rep2


title: P12, Input for P12 H3K27me3 rep3


title: P12, Input for P12 H3K27me3 rep4


title: P7 Neurod1-bacTRAP, rep4

description:
P7_Neurod1_TRAP_rep4
RNAseq_counts.csv


title: P7, Input for P7 H3K27me3 rep3


title: P21, H3K27me3, rep4

description:
P21_H3K27me3_rep4
ChIPseq_TSS_counts.csv


title: P21, H3K27me3, rep5

description:
P21_H3K27me3_rep5
ChIPseq_TSS_counts.csv


title: P7, Input for P7 H3K27me3 rep1 and rep2


title: P21, H3K27me3, rep3

description:
P21_H3K27me3_rep3
ChIPseq_TSS_counts.csv


title: P7 Neurod1-bacTRAP, rep1

description:
P7_Neurod1_TRAP_rep1
RNAseq_counts.csv


title: P21, H3K27me3, rep2

description:
P21_H3K27me3_rep2
ChIPseq_TSS_counts.csv


title: P12, H3K27me3, rep4

description:
P12_H3K27me3_rep4
ChIPseq_TSS_counts.csv


title: P21, Input for P21 H3K27me3 rep1 and rep2


title: P21, H3K27me3, rep1

description:
P21_H3K27me3_rep1
ChIPseq_TSS_counts.csv


title: P7, Input for P7 H3K27me3 rep4


title: P21, Input for P21 H3K27me3 rep5


title: P12, H3K27me3, rep3

description:
P12_H3K27me3_rep3
ChIPseq_TSS_counts.csv


title: P12, H3K27me3, rep1

description:
P12_H3K27me3_rep1
ChIPseq_TSS_counts.csv


title: P12, H3K27me3, rep2

description:
P12_H3K27me3_rep2
ChIPseq_TSS_counts.csv


title: P7, Input for P7 H3K27me3 rep5


title: P7, H3K27me3, rep5

description:
P7_H3K27me3_rep5
ChIPseq_TSS_counts.csv


title: P21, Input for P21 H3K4me3 rep1


title: P7, Input for P7 H3K4me3 rep3


title: P21, Input for P21 H3K4me3 rep2


title: P7, H3K27me3, rep1

description:
P7_H3K27me3_rep1
ChIPseq_TSS_counts.csv


title: P7, H3K27me3, rep2

description:
P7_H3K27me3_rep2
ChIPseq_TSS_counts.csv


title: P12, Input for P12 H3K4me3 rep1


title: P7, H3K27me3, rep3

description:
P7_H3K27me3_rep3
ChIPseq_TSS_counts.csv


title: P7, H3K4me3, rep2

description:
P7_H3K4me3_rep2
ChIPseq_TSS_counts.csv

value: H3K4me3 (Active Motif 39159)


title: P7, Input for P7 H3K4me3 rep2


title: P7, H3K27me3, rep4

description:
P7_H3K27me3_rep4
ChIPseq_TSS_counts.csv


title: P12, H3K4me3, rep2

description:
P12_H3K4me3_rep2
ChIPseq_TSS_counts.csv


title: P12, Input for P12 H3K4me3 rep2


title: P7, Input for P7 H3K4me3 rep1


title: P21, H3K4me3, rep2

description:
P21_H3K4me3_rep2
ChIPseq_TSS_counts.csv


title: P12, H3K4me3, rep1

description:
P12_H3K4me3_rep1
ChIPseq_TSS_counts.csv


title: P7, H3K4me3, rep3

description:
P7_H3K4me3_rep3
ChIPseq_TSS_counts.csv


title: P7, H3K4me3, rep1

description:
P7_H3K4me3_rep1
ChIPseq_TSS_counts.csv


title: SCAR_439_strandedInputforH3K27me3_MCM2Series_T0_r3

description: alternative to: GSM5858931

library_source: other

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Assembly: mm10
Supplementary files format and content: SCAR-seq Partition scores in bed format

molecule: other

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE.

extract_protocol: After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min (MCM2Series: 15 min) and then  collected (T0)

value: Embryonic stem cells

tag: mouse line

value: EdU-labelled genomic DNA (15min)


title: SCAR_438_strandedInputforH3K27me3_MCM2Series_T0_r2

description: alternative to: GSM5858928


title: SCAR_410_strandedInputforH3K27me3_MCM2Series_T0_r2

description: alternative to: GSM5858925


title: SCAR_410_strandedInputforH3K27me3_MCM2Series_T0_r1

description: alternative to: GSM4670133


title: SCAR_438_strandedInputforH3K27me3_MCM2Series_T0_r1

description: alternative to: GSM4670136


title: SCAR_552_H3K27me3_Pole4Series_T0_r2

description: alternative to: GSM5858965

value: EdU-labelled genomic DNA (10min)


title: SCAR_410_H3K27me3_MCM2Series_T0_r2

description: alternative to: GSM4670106


title: SCAR_439_H3K27me3_MCM2Series_T0_r3

description: alternative to: GSM4670112


title: SCAR_552_H3K27me3_Pole4Series_T0_r1

description: alternative to: GSM5858959


title: P21, H3K4me3, rep1

description:
P21_H3K4me3_rep1
ChIPseq_TSS_counts.csv

value: cerebellum


title: SCAR_410_H3K27me3_MCM2Series_T0_r1

description: alternative to: GSM4670097


title: SCAR_438_H3K27me3_MCM2Series_T0_r2

description: alternative to: GSM4670109


title: SCAR_438_H3K27me3_MCM2Series_T0_r1

description: alternative to: GSM4670100


title: SCAR_410_H3K27me3_Pole4Series_T0_r1

description: alternative to: GSM5858955


title: SCAR_552_H4K20me0_Pole4Series_T0_r2

description: alternative to: GSM5858966


title: SCAR_410_H3K27me3_Pole4Series_T0_r2

description: alternative to: GSM5858961


title: SCAR_410_H4K20me0_Pole4Series_T0_r1

description: alternative to: GSM5858956


title: xSCAR_570_strandedInput_JARID2_T0_IAA_rep2

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Assembly: mm10
Supplementary files format and content: SCAR-seq Partition scores in bed format
Library strategy: SCAR-seq

extract_protocol:
For SCAR samples: After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced. For xSCAR samples (H2A.Z, H4K20me0 when indicated, JARID2): cells were crosslinked for 10min with 1% formaldehyde, quenched, nuclei extracted and sonicated using Covaris. Sequentially, fragments were immunoprecipitated, purified, fragments were converted to libraries, biotinylated and EdU-biotin fragments were pulled-down and sequenced.
OTHER

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min (JARID2 xSCAR and Input datasets: 30min) and then either collected (T0) or cultured for indicated maturation intervals (T30; T3; T8) in media without EdU before collection. If treated with DMSO or Indole-3-acetic acid (IAA), cells were incubated for 1h50 with 500uM IAA or DMSO prior to incubation with EdU for 10 min and then either collected (T0) or cultured for indicated timed in media without EdU but continuously with IAA or DMSO

value: Ring1B-mAID Ring1AKO MCM2-2A

value: EdU-labelled genomic DNA


title: xSCAR_570_strandedInput_JARID2_T0_DMSO_rep2


title: SCAR_551_H3K27me3_Pole4Series_T0_r2

description: alternative to: GSM5858963


title: SCAR_551_H4K20me0_Pole4Series_T0_r1

description: alternative to: GSM5858958


title: SCAR_410_H4K20me0_Pole4Series_T0_r2

description: alternative to: GSM5858962


title: xSCAR_570_JARID2_T0_DMSO_rep2


title: SCAR_551_H4K20me0_Pole4Series_T0_r2

description: alternative to: GSM5858964


title: xSCAR_570_JARID2_T0_IAA_rep2


title: xSCAR_570_JARID2_T0_DMSO_rep1


title: xSCAR_570_JARID2_T0_IAA_rep1


title: xSCAR_570_strandedInput_JARID2_T0_DMSO_rep1


title: xSCAR_579_strandedInput_T0_r2


title: xSCAR_579_strandedInput_T0_r1


title: xSCAR_551_strandedInput_T0_r2


title: xSCAR_442_strandedInput_T0_r1


title: xSCAR_410_strandedInput_T0_r2

value: wildtype


title: xSCAR_551_strandedInput_T0_r1


title: SCAR_551_H3K27me3_Pole4Series_T0_r1

description: alternative to: GSM5858957


title: SCAR_552_H4K20me0_Pole4Series_T0_r1

description: alternative to: GSM5858960


title: xSCAR_579_H4K20me0_T0_r2


title: xSCAR_579_H4K20me0_T0_r1


title: xSCAR_442_H4K20me0_T0_r2


title: xSCAR_442_H4K20me0_T0_r1


title: xSCAR_442_strandedInput_T0_r2


title: xSCAR_551_H4K20me0_T0_r2


title: xSCAR_410_H4K20me0_T0_r1


title: SCAR_476_H4K20me0_Pola1Series_T0_r2


title: xSCAR_551_H4K20me0_T0_r1


title: xSCAR_410_H2AZ_T0_r2_A+B


title: SCAR_438_H4K20me0_MCM2Series_T0_r2


title: ChIP_Input_H3K27me3_IAA_rep2

description: .bw file for all replicates is included on R1 sample.

value: Ring1AKO Ring1BmAID MCM2-2A

value: Indole-3-acetic (IAA) 500uM for 120min


title: xSCAR_442_H2AZ_T0_r2_A+B


title: xSCAR_579_H2AZ_T0_r1


title: xSCAR_579_H2AZ_T0_r2_A+B


title: xSCAR_410_H4K20me0_T0_r2


title: ChIP_Input_H3K27me3_DMSO_rep2


title: ChIP_Input_H3K27me3_IAA_rep1


title: ChIP_Input_H3K27me3_DMSO_rep1


title: xSCAR_410_strandedInput_T0_r1


title: SCAR_438_H4K20me0_MCM2Series_T0_r1


title: xSCAR_551_H2AZ_T0_r1


title: ChIP_H3K27me3_DMSO_rep1


title: ChIP_Input_JARID2_IAA_rep2


title: ChIP_H3K27me3_IAA_rep2


title: ChIP_Input_JARID2_IAA_rep1


title: ChIP_H3K27me3_IAA_rep1


title: SCAR_476_H4K20me0_Pola1Series_T0_r1


title: SCAR_442_H4K20me0_MCM2Series_T0_r3


title: SCAR_579_H4K20me0_Pola1Series_T0_r3


title: xSCAR_410_H2AZ_T0_r1


title: xSCAR_442_H2AZ_T0_r1


title: ChIP_H3K27me3_DMSO_rep2


title: ChIP_Input_JARID2_DMSO_rep2


title: ChIP_Input_JARID2_DMSO_rep1


title: ChIP_JARID2_IAA_rep2


title: ChIP_JARID2_IAA_rep1


title: ChIP_JARID2_DMSO_rep2


title: ChIP_JARID2_DMSO_rep1


title: IR_3

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

data_processing:
The FastQC tool (version 0.11.8) was used for quality control to determine low quality and adaptor portion of the reads for trimming.
Trimmomatic (version 0.39) was used for read-trimming.
Trimmed reads were aligned to the mouse reference genome (mm10) using HiSAT2 (version 2.1.0, default settings).
Count matrix for each sample was produced by counting aligned reads using featureCounts (version 1.6.2).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw count values for each Sample.

source_name: Heart

extract_protocol:
RNeasy Micro Kit (Qiagen) was used to isolate RNA from whole hearts, according to manufacturer’s recommendations.
KAPA mRNA HyperPrep kit (Kapa Biosystems) was used according to the manufacturer's instructions to prepare the RNA sequencing libraries.

value: Heart

value: WT

value: Male

tag: age

value: 17 weeks

value: IR without any injection at 12 weeks of age


title: IR_1


title: IR-Sham_2

value: Sham surgery without any injection at 12 weeks of age


title: IR-Edit_4

value: IR and injection of a functional CaMKIIdelta editing system at 12 weeks of age


title: Cryosection nr. 2 from patient P13. Granuloma biopsy taken at visit V02

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

data_processing:
10x genomics V3.0.2 cellranger mkfastq
10x genomics V1.2.0 spaceranger count
10x genomics V1.2.0 spaceranger aggr
custom Python notebook used to convert the matrix from cellranger into csv format (without additional processing), generate QC metrics and metadata files (see project repository)
Genome_build: GRCh38
Supplementary_files_format_and_content: ST_GEO_raw_counts.csv.gz is a comma-separated, gzipped file containing a Cells (rows) x Genes (columns) raw counts matrix (includes header and row names)
Supplementary_files_format_and_content: ST_GEO_spots.csv.gz is a comma-separated text file containing single spot metadata: sample of origin, QC metrics and spot location
Supplementary_files_format_and_content: ST_GEO_genes.csv.gz is a comma-separated text file containing genes names and ESEMBL gene IDs

source_name: Biopsy from cutaneous granuloma

extract_protocol:
6mm punch-biopsies were taken from affected skin as well as skin presenting no signs of inflammation before treatment. Sarcoidosis has been histologically and clinically confirmed by trained dermatologists. Fresh biopsies were embedded in optimal cutting temperature (OCT) compound and stored as sectioning blocks at -80 °C until further processing. Before undertaking the full protocol, a tissue optimization experiment (10x Genomics, Visium Spatial Tissue Optimization) was performed using cryosections of patient skin biopsies with imaging of fluorescence signal identifying 18 minutes as optimum permeabilization time.
Spatial transcriptomic libraries were generated using the Visium Spatial gene expression reagent kit (10x Genomics) according to the manufacturer’s protocol.
The sequencing-ready spatial transcriptomics libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, using the Illumina Novaseq platform and the 75 bp paired-end configuration.

tag: batch

tag: patient

tag: visit

tag: section nr.


title: IR_2

tag: strain

tag: genotype

tag: treatment


title: IR-Edit_3

tag: tissue

tag: Sex


title: IR-Sham_1


title: IR-Virus control_2

value: IR and injection of a control virus at 12 weeks of age


title: IR-Sham_3


title: IR-Edit_1


title: IR-Virus control_1


title: Cryosection nr. 1 from patient P13. Granuloma biopsy taken at visit V02

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences


title: IR-Edit_2


title: SCAR_580_strandedInput_T8_IAA_r3

description: EdU-labelled genomic DNA

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Assembly: mm10
Supplementary files format and content: SCAR-seq Partition scores in bigwig format
Library strategy: SCAR-Seq

source_name: Embryonic stem cells

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min and then either collected (T0) or cultured for indicated maturation intervals (T30; T3; T8) in media without EdU before collection. If treated with DMSO or Indole-3-acetic acid (IAA), cells were incubated for 1h50 with 500uM IAA or DMSO prior to incubation with EdU for 10 min and then either collected (T0) or cultured for indicated timed in media without EdU but continuously with IAA or DMSO

tag: cell line

value: Ring1B-mAID MCM2-2A Ring1AKO

value: Indole-3-acetic acid (IAA) 500uM


title: SCAR_580_strandedInput_T3_IAA_r3

description: EdU-labelled genomic DNA


title: SCAR_580_strandedInput_T0_IAA_r3

description: EdU-labelled genomic DNA


title: Cryosection nr. 2 from patient P12. Granuloma biopsy taken at visit V02


title: Cryosection nr. 1 from patient P11. Granuloma biopsy taken at visit V02


title: Cryosection nr. 2 from patient P10. Granuloma biopsy taken at visit V02


title: SCAR_580_strandedInput_T8_DMSO_r3

description: EdU-labelled genomic DNA

value: DMSO


title: Cryosection nr. 1 from patient P10. Granuloma biopsy taken at visit V02


title: Cryosection nr. 1 from patient P08. Granuloma biopsy taken at visit V06


title: SCAR_580_strandedInput_T0_DMSO_r3

description: EdU-labelled genomic DNA


title: IR-Virus control_3


title: SCAR_580_strandedInput_T3_DMSO_r3

description: EdU-labelled genomic DNA


title: Cryosection nr. 1 from patient P07. Granuloma biopsy taken at visit V06


title: SCAR_580_H3K27me3_T8_IAA_r3

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T8_IAA_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Cryosection nr. 2 from patient P04. Granuloma biopsy taken at visit V06


title: SCAR_580_H3K27me3_T3_IAA_r3

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T3_IAA_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T8_DMSO_r3

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T8_DMSO_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T3_DMSO_r3

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T3_DMSO_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Cryosection nr. 1 from patient P01. Granuloma biopsy taken at visit V02


title: Cryosection nr. 1 from patient P12. Granuloma biopsy taken at visit V02


title: Cryosection nr. 1 from patient P04. Granuloma biopsy taken at visit V02


title: Cryosection nr. 1 from patient P01. Granuloma biopsy taken at visit V00


title: SCAR_580_H3K27me3_T0_DMSO_r3

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T0_DMSO_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Cryosection nr. 1 from patient P04. Granuloma biopsy taken at visit V06


title: SCAR_580_strandedInput_T8_IAA_r2

description: EdU-labelled genomic DNA


title: SCAR_580_strandedInput_T0_IAA_r2

description: EdU-labelled genomic DNA


title: SCAR_580_strandedInput_T8_DMSO_r2

description: EdU-labelled genomic DNA


title: Cryosection nr. 1 from patient P08. Granuloma biopsy taken at visit V02


title: SCAR_580_strandedInput_T3_IAA_r2

description: EdU-labelled genomic DNA


title: Cryosection nr. 1 from patient P05. Granuloma biopsy taken at visit V02


title: Cryosection nr. 1 from patient P06. Granuloma biopsy taken at visit V06


title: Cryosection nr. 1 from patient P02. Granuloma biopsy taken at visit V06


title: Cryosection nr. 1 from patient P03. Granuloma biopsy taken at visit V02


title: SCAR_580_strandedInput_T3_DMSO_r2

description: EdU-labelled genomic DNA


title: Cryosection nr. 1 from patient P02. Granuloma biopsy taken at visit V02


title: Cryosection nr. 1 from patient P03. Granuloma biopsy taken at visit V06


title: SCAR_580_strandedInput_T0_DMSO_r2

description: EdU-labelled genomic DNA


title: SCAR_580_H3K27me3_T3_IAA_r2

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T3_IAA_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T0_IAA_r3

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T0_IAA_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T8_IAA_r2

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T8_IAA_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T8_DMSO_r2

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T8_DMSO_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T0_IAA_r2

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T0_IAA_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T3_DMSO_r2

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T3_DMSO_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T0_DMSO_r2

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T0_DMSO_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P05 Non-lesional skin sample taken at visit V06

data_processing:
10x genomics V3.0.2 cellranger mkfastq
10x genomics V3.0.2 cellranger count
10x genomics V3.0.2 cellranger aggr
custom Python notebook used to convert the matrix from cellranger into csv format (without additional processing), generate QC metrics and metadata files (see project repository)
Genome_build: GRCh38
Supplementary_files_format_and_content: SC_GEO_raw_counts.csv.gz is a comma-separated, gzipped file containing a Cells (rows) x Genes (columns) raw counts matrix (includes header and row names)
Supplementary_files_format_and_content: SC_GEO_cells.csv.gz is a comma-separated text file containing single cell metadata: sample of origin, quality metrics, QC pass/fail flag
Supplementary_files_format_and_content: SC_GEO_genes.csv.gz is a comma-separated text file containing genes names and ESEMBL gene IDs

source_name: Healthy skin cell suspension

extract_protocol:
6mm punch-biopsies were taken from affected skin as well as skin presenting no signs of inflammation before treatment. Sarcoidosis has been histologically and clinically confirmed by trained dermatologists. Fresh biopsies were digested according to a collagenase IV skin digestion protocol (M. C. Brüggen et al, blood 2014) to generate single-cell suspensions. Single cell suspensions obtained from non-lesional and lesional skin were next incubated with commercially available DNA-labeled antibodies (TotalSeq-A, Biolegend) together with an antibody against CD45 and a cell viability dye at 4 °C for 30 min. Following incubation, cell suspensions were washed three times with PBS containing BSA. After the final wash, cell suspensions were resuspended in PBS containing BSA and a viability dye for discrimination between live and dead cells. Next, 10,000 viable CD45+ and 10,000 viable CD45- cells were sort-purified from non-lesional and lesional skin and those four cell fractions were kept separately on ice and pooled together before being processed as a single sample.
Single-cell libraries were generated using the Chromium Controller and NEXT GEM Single Cell 3′ Reagent Kit v3 or v3.1 (10x Genomics) according to the manufacturer’s protocol.
The sequencing-ready scRNA-seq libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, using the Illumina HiSeq 3000/4000 or the Illumina Novaseq platform (P12_V06, P13_V06) and the 75 bp paired-end configuration.

value: Non-lesional skin


title: Patient P05 Lesional skin sample taken at visit V06

source_name: Cutaneous granuloma cell suspension

value: Lesional skin


title: SCAR_580_strandedInput_T8_IAA_r1

description: EdU-labelled genomic DNA


title: Patient P08 Lesional skin sample taken at visit V06


title: Patient P06 Lesional skin sample taken at visit V06


title: Patient P04 Lesional skin sample taken at visit V06


title: Patient P07 Lesional skin sample taken at visit V06


title: SCAR_580_strandedInput_T3_IAA_r1

description: EdU-labelled genomic DNA


title: Patient P04 Non-lesional skin sample taken at visit V06


title: SCAR_580_strandedInput_T0_IAA_r1

description: EdU-labelled genomic DNA


title: Patient P03 Non-lesional skin sample taken at visit V06


title: SCAR_580_strandedInput_T8_DMSO_r1

description: EdU-labelled genomic DNA


title: Patient P11 Lesional skin sample taken at visit V06


title: Patient P03 Lesional skin sample taken at visit V06


title: SCAR_580_strandedInput_T3_DMSO_r1

description: EdU-labelled genomic DNA


title: SCAR_580_H3K27me3_T3_IAA_r1

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T3_IAA_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P13 Non-lesional skin sample taken at visit V02


title: Patient P02 Lesional skin sample taken at visit V06


title: Patient P02 Non-lesional skin sample taken at visit V06


title: Patient P13 Lesional skin sample taken at visit V02


title: SCAR_580_H3K27me3_T8_IAA_r1

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T8_IAA_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P12 Non-lesional skin sample taken at visit V02


title: SCAR_580_H3K27me3_T0_IAA_r1

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T0_IAA_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P12 Lesional skin sample taken at visit V02


title: Patient P11 Non-lesional skin sample taken at visit V02


title: SCAR_580_H3K27me3_T8_DMSO_r1

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T8_DMSO_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P11 Lesional skin sample taken at visit V02


title: SCAR_580_H3K27me3_T3_DMSO_r1

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T3_DMSO_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_580_H3K27me3_T0_DMSO_r1

description:
EdU-labelled genomic DNA
SCAR_580_H3K27me3_T0_DMSO_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_476_strandedInput_Pola1Series_T0_r3

description: EdU-labelled genomic DNA


title: SCAR_476_strandedInput_Pola1Series_T0_r1

description: EdU-labelled genomic DNA


title: SCAR_476_strandedInput_Pola1Series_T0_r2

description: EdU-labelled genomic DNA


title: SCAR_580_strandedInput_T0_DMSO_r1

description: EdU-labelled genomic DNA


title: SCAR_579_strandedInput_Pola1Series_T0_r3

description: EdU-labelled genomic DNA


title: Patient P10 Lesional skin sample taken at visit V02


title: Patient P10 Non-lesional skin sample taken at visit V02


title: SCAR_410_strandedInput_Pola1Series_T0_r3

description: EdU-labelled genomic DNA


title: Patient P08 Lesional skin sample taken at visit V02


title: Patient P07 Lesional skin sample taken at visit V02


title: Patient P07 Non-lesional skin sample taken at visit V02


title: SCAR_410_strandedInput_Pola1Series_T0_r2

description: EdU-labelled genomic DNA


title: Patient P06 Non-lesional skin sample taken at visit V02


title: SCAR_410_strandedInput_Pola1Series_T0_r1

description: EdU-labelled genomic DNA


title: Patient P05 Lesional skin sample taken at visit V02


title: Patient P06 Lesional skin sample taken at visit V02


title: SCAR_410_H4K20me0_Pola1Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_410_H4K20me0_Pola1Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_476_H2AK119ub_Pola1Series_T0_r3

description:
EdU-labelled genomic DNA
SCAR_476_H2AK119ub_Pola1Series_T0_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_476_H2AK119ub_Pola1Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_476_H2AK119ub_Pola1Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_410_H4K20me0_Pola1Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_410_H4K20me0_Pola1Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_579_H2AK119ub_Pola1Series_T0_r3

description:
EdU-labelled genomic DNA
SCAR_579_H2AK119ub_Pola1Series_T0_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_476_H2AK119ub_Pola1Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_476_H2AK119ub_Pola1Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P08 Non-lesional skin sample taken at visit V02


title: Patient P03 Non-lesional skin sample taken at visit V02


title: SCAR_410_H2AK119ub_Pola1Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_Pola1Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P02 Lesional skin sample taken at visit V02


title: Patient P05 Non-lesional skin sample taken at visit V02


title: SCAR_410_H2AK119ub_Pola1Series_T0_r3

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_Pola1Series_T0_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: xSCAR_570_strandedInput_JARID2_T0_IAA_rep1

value: Ring1B-mAID Ring1AKO MCM2-2A

value: EdU-labelled genomic DNA


title: Patient P03 Lesional skin sample taken at visit V02


title: Patient P01 Non-lesional skin sample taken at visit V02


title: SCAR_410_H2AK119ub_Pola1Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_410_H2AK119ub_Pola1Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed

value: wildtype


title: SCAR_579_H3K27me3_Pola1Series_T0_r3

description:
EdU-labelled genomic DNA
SCAR_579_H3K27me3_Pola1Series_T0_r3.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P01 Lesional skin sample taken at visit V02


title: Patient P01 Lesional skin sample taken at visit V00


title: SCAR_476_H3K27me3_Pola1Series_T0_r1

description:
EdU-labelled genomic DNA
SCAR_476_H3K27me3_Pola1Series_T0_r1.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: SCAR_476_H3K27me3_Pola1Series_T0_r2

description:
EdU-labelled genomic DNA
SCAR_476_H3K27me3_Pola1Series_T0_r2.nodup.mm10_SE_minusinput_smooth_results_w1000_s30_d30_z1_RFD.bed


title: Patient P01 Non-lesional skin sample taken at visit V00