title: scRNA-seq of patient 4 tumor sample

city: Innsbruck

first: Georgios

last: Fotakis

state: Tyrol

address: Innrain 80-82

department: Bioinformatics

institute: Medical University Innsbruck

data_processing:
scRNA-seq: FASTQ files were processed with cellranger v3.1
Bulk RNA-seq: FASTQ files were pre-processed using Trimmomatic V0.36 to trim long reads to a maximum length of 200 bp
Bulk RNA-seq: The pre-processed reads were then aligned to the reference genome using STAR v2.5.3a
Bulk RNA-seq: Read counts were generated using htseq-count v0.12.3
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNA-seq: TSV files containing  detected cellular barcodes (barcodes.tsv) and  correspondig genes (features.tsv) as returned from cellranger
Supplementary_files_format_and_content: scRNA-seq: MTX sparse matrix containing counts as returned from cellranger
Supplementary_files_format_and_content: Bulk RNA-seq: tab-delimited text files include gene count values for each bulk RNA-seq sample

source_name: Adenocarcinoma with cribriform and solid pattern

extract_protocol:
Paired malignant and benign 1x1 cm tissue biopsies were extracted within one hour after surgery from prostate specimens using punch needles. The biopsies were rinsed with PBS, minced into 1mm3 pieces and transferred to the 5 ml of digestion solution ((DMEM high glucose (Sigma-Aldrich) supplemented with with L-glutamine-penicillin-streptomycin (100 U/ml) (Sigma-Aldrich), 20 uL DNase (Quiagen) (75 U/ml), 2 mL Collagenase V (2 %) (Sigma-Aldrich) and Dispase II (2.5 U/mL) (Gibco)) for 45 minutes in water bath (37 °C).
After tissue digestion and preparaing single cell suspension, viable cells were sorted and proceeded for single cell capture using the Chromium Controller (10X Genomics). Barcoding and library preparation was performed using Chromium Next GEM single cell 3’ kit (v3.1, 10x Genomics) according to the manufacturer’s recommendations. For each sample, an input of ~17,000 cells was used to finally recover 10000 cells. The resulting 3‘ Gene Expression libraries were sequenced on Illumina HiSeq 4000 at a sequencing depth of 50000 reads per cell.


title: MAC_TEDseq_LPS 4h_rep1

status: Public on Jun 27 2022

type: SRA

city: Ithaca

first: Andrew

last: Grimson

state: New York

address: Biotechnology building, 526 campus road,  room 445

department: Molecular biology and genetics

country: USA

institute: Cornell University

description: processed data: PASisoforms_summary_rep1.txt

library_source: transcriptomic

data_processing:
Library strategy: TED-seq
RTA v2 software used for basecalling on NextSeq 500 and HiSeq 4000.
After poly-(A) tail trimming, the reads with the length shorter than 15 nucleotides and mean quality score below 20 were filtered out. After PCR duplicates were removed based on UMI barcode, the remaining sequences were mapped to hg38 whole genome using STAR (2.4.2a).  For spike-in genome mapping, BWA was used.
The mapped reads were represented by their 5' terminal  posistions on the same strand, and converted into BED format.
After identifying which transcript isoform a TED-seq read is derived from, we estimated poly(A) tail length by subtracting the distance between the 5' end of a TED-seq read and the cleavage and polyadenylation site of the corresponding transcript isoform from 300 nucleotides (insert size). For the transcript isoforms that have TED-seq reads more than 50 within 300 nucleotide window upstream of the cleavage and polyadenylation site, ,ean of  poly(A) tail lengths was used to represent poly(A) tail length distributions for transcripts derived from a transcript isoform.
Genome_build: hg38
Supplementary_files_format_and_content: PROseq_rep1.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: PROseq_rep2.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: peaks.txt: matrix_Identification of 3′-seq peak positions  with more than 5 CPM.
Supplementary_files_format_and_content: Readcounts_peak.txt: matrix_Normalized abundance (CPM) per the identified 3′-seq peak positions.
Supplementary_files_format_and_content: PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: Integrated_datasets.txt: matrix_Transcription in RPKM, mRNA level in CPM, and mean poly(A) tail length for every transcript isoform for the actinomycin D-untrreated conditions.

molecule: total RNA

organism: Homo sapiens

source_name: Monocyte-derived macrophage cells

growth_protocol: THP-1 cells were cultured in RPMI1640 supplemented with 10% FBS and 1% antibiotics.

extract_protocol:
After washing the cells with DPBS three times, total RNA was extracted by directly adding TRIzol  to the plate with the adherent cells on it. 5 million cells were used for the construction of PRO-seq libraries. For 3′-seq and TED-seq, 10 ug of total RNAs were used.
RNA libraries were prepared to be compatible with Illumina small RNA sequencing.
We prepared TED-seq libraries as described in Woo et. al. (2018) Cell Reports.

treatment_protocol: THP-1 cells were differentiated to macrophage-like cells by incubating them overnight in the 200 ng/ml PMA-containing (sigma Aldrich, P1585-1MG) complete media, followed by 3 days incubation in fresh media without PMA. The resulting differentiated cells were stimulated with 200 ng/mL LPS and collected at four consecutive time points 0 (no stimulation), 1, 2, and 4 hours.

tag: cell state

value: Differentiated into macrophage-like state

tag: cell type

value: Monocyte

tag: cell line

tag: treatment

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h, followed by treatment with LPS for 2 hour.


title: Group4-21-m

city: Huddinge

first: Ani

last: Azatyan

state: Stockholm

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Basecalling and demultiplexing were performed using bcl2fastq (v2.20.0).
Quality and adapter trimming of reads were performed using TrimGalore (v0.6.4).
standard mRNA detection: reads from the poly(A) enriched fraction were aligned to the Gencode GRCh38 reference genome assembly using the Star (v2.5.2) aligner. Counts were assigned to genes using featureCounts (v1.5.1)
circRNA detection: reads from the circRNA enriched fraction were analysed with the CIRCexplorer2 characterization pipeline to identify circular back spliced junctions and aligned to Gencode GRCh38 using CIRCexplorer2/Star (PMID: 27365365) with the default parameters.
linear back spliced transcript detection: reads from poly(A) enriched fraction were analysed with the CIRCexplorer2 characterization pipeline to identify linear back spliced junctions and aligned to Gencode GRCh38 using CIRCexplorer2/Star (PMID: 27365365) with the default parameters.
Fusion detections: reads from the poly(A) enriched fraction and circRNA enriched fraction were aligned to Gencode GRCh38 using Star-Fusion (PMID: 31639029) with the default parameters.
Normalized counts were generated using DESeq2 (v1.32.0).
Assembly: GRCh38
Supplementary files format and content: tab delimited text file with raw mRNA counts for every sample generated by featureCounts
Supplementary files format and content: tab delimited text file with raw circRNA counts for every sample generated by CIRCexplorer2
Supplementary files format and content: tab delimited text file with raw fusion transcript counts for every sample generated by StarFusion

molecule: polyA RNA

source_name: Medullobalstoma Group 4

extract_protocol:
The medulloblastoma tumor RNA samples were provided by the Childhood Brain Tumor Tissue Consortium (www.cbttc.org), and 5 normal cerebellum RNA samples were purchased commercially from Takara (Japan), Amsbio (UK) or BioChain (USA).
mRNA / poly(A) enriched fraction: ≈ 100 ng of total RNA was used to generate stranded mRNA libraries with the TruSeq®Stranded mRNA Low Throughput Sample Preparation kit according to the manufacturer’s instructions (15031047, Illumina, USA). This protocol involves a poly(A) selection/enrichment and ribosomal RNA depletion step.
circRNA / (poly(A-) / RNaseR+)  fraction: 1 μg of total RNA was used. First, ribosomal RNA was depleted using the RiboMinusTM Eukaryote System V2 (Ambion) (A15026, ThermoFisher USA), followed by digestion with 5U RNase R for 1 hr to degrade linear RNAs and purification with the RNeasy MinElute Cleanup Kit (74204, Qiagen). The concentration and quality of the enriched circRNA RiboMinus/RNase R preparations were assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). 1 ng of RiboMinus/RNase R treated RNA was used for cDNA library generation. Random hexamer primers and Superscript III reverse transcriptase (18080055, Invitrogen, USA) were used for 1st strand synthesis and stranded mRNA library was generated according to the TruSeq®Stranded mRNA Low Throughput Sample Preparation protocol (15031047, Illumina, USA). The concentration and quality of the cDNA libraries were assessed with Qubit (Life Technologies, USA) and TapeStation, respectively.

tag: disease state

value: Medulloblastoma

tag: sample location

value: Cerebellum/Posterior Fossa

tag: medulloblastoma subgroup

tag: biospecimen id

tag: research subject id

tag: molecule subtype

value: mRNA / poly(A)


title: Vav-cre-Tcf7KO-DN1_BC_35

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

country: China

institute: China Agricultural University

description:
PolyA RNA
processed data file: barcode_information.xlsx
processed data file: count_matrix.csv
processed data file: expression_matrix_log2(TPM:10+1).csv

data_processing:
Unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails.
Next, we removed reads with adapter contaminants and low-quality bases (N>10%).
The cleaned reads were aligned to the mm10 mouse transcriptome (Genocode) using Tophat (version 2.1.1).
Uniquely mapped reads were counted using htseq-count of the HTSeq package. For each gene, duplicated transcripts with the same UMI sequence were removed. For each cell, the transcript copy number of each gene were counted on the basis of the number of distinct UMIs of that gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcode_information.xlsx
Supplementary_files_format_and_content: count_matrix.csv
Supplementary_files_format_and_content: expression_matrix_log2(TPM:10+1).csv

organism: Mus musculus

source_name: thymus DN1 cells (CD45+Lin-CD4-CD8-CD25-CD44+)

extract_protocol:
Single-cell cDNA amplification was carried out by using the STRT protocol with several modifications to allow for multiplexed single-cell RNA-seq. Libraries were prepared using KAPA Hyper Prep Kits (KK8505). The NEB U-shaped adapter was used for ligation. The libraries were sequenced on an Illumina Hiseq x ten platform to generate 150-bp paired-end reads (sequenced by BGI).
Libraries are constructed according to the standard protocol for Smart-seq2.

tag: strain/background

tag: genotype/variation

value: Vav-cre; Tcf7fl/fl

tag: tissue

value: thymus

tag: age

value: 6~8 wks


title: MAC_TEDseq_LPS 2h_rep1

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h.


title: Group4-22-m


title: Group4-20-m


title: MAC_TEDseq_LPS 1h_rep2

description: processed data: PASisoforms_summary_rep2.txt

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h, followed by treatment with LPS for 4 hour.


title: scRNA-seq of patient 3 tumor sample

country: Austria

source_name: Adenocarcinoma with cribriform and acinar pattern


title: scRNA-seq of patient 1 tumor sample

source_name: Adenocarcinoma with cribriform pattern


title: MAC_TEDseq_LPS 2h_rep2

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h, followed by treatment with LPS for 1 hour


title: Vav-cre-Tcf7KO-DN1_BC_33


title: scRNA-seq of patient 2 tumor sample


title: Vav-cre-Tcf7KO-DN1_BC_32


title: MAC_TEDseq_LPS 1h_rep1


title: Group4-19-m


title: Vav-cre-Tcf7KO-DN1_BC_31


title: scRNA-seq of patient 2 benign sample

source_name: patient 2 benign sample

value: Benign


title: Vav-cre-Tcf7KO-DN1_BC_2


title: scRNA-seq of patient 4 benign sample

source_name: patient 4 benign sample


title: MAC_TEDseq_LPS 0h_rep1


title: MAC_TEDseq_LPS 0h_rep2


title: scRNA-seq of patient 3 benign sample

source_name: patient 3 benign sample


title: Group4-17-m


title: Vav-cre-Tcf7KO-DN1_BC_30


title: Group4-18-m

value: Ventricles


title: MAC_PROseq_LPS 4h_rep1

description: processed data: PROseq_rep1.txt

data_processing:
Library strategy: PRO-seq
RTA v2 software used for basecalling on NextSeq 500 and HiSeq 4000.
Adaptor squencess were trimmed using Cutadapt. The resulting reads were deduplicated based on UMI barcodes, and mapped to hg38 whole genome using BWA.
Actual RNA polymerase position was summarised by representing each mapped read by its 5' terminal position on the opposite strand, and converted into BED format.
Reads per kilobase per million mapped (RPKM) was calculated to quantify transcription activity per gene using GENCODE V26 human transcriptome annotation.
Genome_build: hg38
Supplementary_files_format_and_content: PROseq_rep1.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: PROseq_rep2.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: peaks.txt: matrix_Identification of 3′-seq peak positions  with more than 5 CPM.
Supplementary_files_format_and_content: Readcounts_peak.txt: matrix_Normalized abundance (CPM) per the identified 3′-seq peak positions.
Supplementary_files_format_and_content: PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: Integrated_datasets.txt: matrix_Transcription in RPKM, mRNA level in CPM, and mean poly(A) tail length for every transcript isoform for the actinomycin D-untrreated conditions.

extract_protocol:
After washing the cells with DPBS three times, total RNA was extracted by directly adding TRIzol  to the plate with the adherent cells on it. 5 million cells were used for the construction of PRO-seq libraries. For 3′-seq and TED-seq, 10 ug of total RNAs were used.
RNA libraries were prepared to be compatible with Illumina small RNA sequencing.
We prepared PRO-seq libraries as described in Kwak et. al. (2013) Science.


title: Vav-cre-Tcf7KO-DN1_BC_29


title: Vav-cre-Tcf7KO-DN1_BC_28


title: Group4-16-m


title: scRNA-seq of patient 1 benign sample

source_name: patient 1 benign sample


title: MAC_PROseq_LPS 2h_rep2

description: processed data: PROseq_rep2.txt


title: Vav-cre-Tcf7KO-DN1_BC_27


title: Group4-15-m


title: DIPGVI-C30-Rx_cells_ChIP1_Input_1

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

library_source: genomic

data_processing:
ChIP-seq datasets were processed using the ChIP-seq module of GenPipes (v3.1.0 for isogenic cell lines, v3.1.2 for parental cell lines). Raw reads were trimmed using Trimmomatic (v0.32) to remove adaptor and sequencing-primer associated reads then aligned to hg19 using bwa-mem (v0.7.12) with default parameters. PCR duplicate reads as defined by reads with identical mapping coordinates were then collapsed by Picard (v2.0.1) to produce uniquely aligned reads. Reads with a mapping quality of 5 or less were then filtered out. For single-end (SE) 50bp datasets, reads were extended by 250bp.
Wiggle tracks are generated using uniquely aligned reads using Homer (v4.9.1). ChIP-seq RPKM values over CGIs and genome-wide 100kb bins for scatterplots were calculated using VisRSeq (v0.9.40).
Rx- and RPKM-normalized BigWig tracks were produced using the “bamCoverage” functionality of deeptools (v3.5.1). Rx ratios were supplied via the ‘--scaleFactor’ option.  Reads flagged as duplicates, mapping to random, mitochondrial or sex chromosomes, as well as low-mappability regions according to ENCODE’s blacklist were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files. Read coverage for each sample over the human genome

molecule: genomic DNA

source_name: Pons

extract_protocol:
Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP or HyperPrep Illumina library preparation reagents. Ffor HTP kit, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adapter ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, at 20°C for 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. For HyperPrep kit, end-repair and A tailing were performed in one reaction: 15ul of ChIP sample was incubated with 45ul end repair+A-tailing mix at 20°C for 30 min, then 65°C for 30 min. Directly proceeded to adapter ligation by adding 5ul of IDT for Illumina Unique Dual Indexes (IDT) adapters and 45ul ligation buffer enzyme mix, incubating at 20°C for 15 min, followed by Ampure XP bead purification. Library enrichment: 10 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: material

value: Cell line

tag: histone mark/factor

value: Input

tag: crispr

value: Parental

tag: clone or passage


title: MAC_PROseq_LPS 2h_rep1

description: processed data: PROseq_rep1.txt

tag: cell state

value: Differentiated into macrophage-like state

tag: cell type


title: DIPG007p149-Rx_cells_ChIP1_Input_1


title: Group4-13-m


title: Group4-14-m


title: MAC_PROseq_LPS 4h_rep2

description: processed data: PROseq_rep2.txt

value: Monocyte

tag: cell line

tag: treatment


title: BT869p21-Rx_cells_ChIP1_Input_1


title: Vav-cre-Tcf7KO-DN1_BC_26


title: MAC_PROseq_LPS 1h_rep1

description: processed data: PROseq_rep1.txt

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h, followed by treatment with LPS for 2 hour.


title: MAC_PROseq_LPS 1h_rep2

description: processed data: PROseq_rep2.txt


title: Vav-cre-Tcf7KO-DN1_BC_25


title: BT245_KO_c5p8_Input

source_name: Thalamus

value: KO


title: MAC_PROseq_LPS 0h_rep2

description: processed data: PROseq_rep2.txt


title: Group4-12-m

tag: disease state

value: Medulloblastoma

tag: sample location

value: Cerebellum/Posterior Fossa


title: Group4-10-m

tag: medulloblastoma subgroup

tag: biospecimen id

value: mRNA / poly(A)


title: Group4-11-m

tag: research subject id

tag: molecule subtype


title: Vav-cre-Tcf7KO-DN1_BC_24

tag: strain/background

tag: genotype/variation

value: Vav-cre; Tcf7fl/fl

value: thymus


title: MAC_3′seq_LPS 2h_rep2

description:
processed data: peaks.txt
processed data: Readcounts_peak.txt

data_processing:
Library strategy: 3′-seq
RTA v2 software used for basecalling on NextSeq 500 and HiSeq 4000.
5′ RNA adaptor sequence was removed from the 3′ end of sequencing reads using Cutadapt with option -e 0.10, --overlap 2, --minimum-length=10, --nextseq-trim 20. After adaptor removal, reads with at least one quality score below 20 were filtered out. The first 30 nucleotides containing UMI barcode of 8 nucleotides were used to deduplicate the reads. After trimming 16 nucleotides (8-mer UMI barcode and 8-mer dTs) off of the 5′ end, the remaining reads with minimum 10 nucleotides were finally mapped to hg38 human genome using STAR.
The aligned reads were represented by their 5′ end mapping position on the opposite strand, and converted to a BedGraph format
The mapping position and the corresponding read counts of a 3′-seq peak were used to determine the cleavage and polyadenylation site and mRNA abundance of a transcript isoform.  We defined the 3'seq position with the totalled readcounts  across all samples more than 5 CPMs as the actually expressed PAS isoforms.
Genome_build: hg38
Supplementary_files_format_and_content: PROseq_rep1.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: PROseq_rep2.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: peaks.txt: matrix_Identification of 3′-seq peak positions  with more than 5 CPM.
Supplementary_files_format_and_content: Readcounts_peak.txt: matrix_Normalized abundance (CPM) per the identified 3′-seq peak positions.
Supplementary_files_format_and_content: PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: Integrated_datasets.txt: matrix_Transcription in RPKM, mRNA level in CPM, and mean poly(A) tail length for every transcript isoform for the actinomycin D-untrreated conditions.

extract_protocol:
After washing the cells with DPBS three times, total RNA was extracted by directly adding TRIzol  to the plate with the adherent cells on it. 5 million cells were used for the construction of PRO-seq libraries. For 3′-seq and TED-seq, 10 ug of total RNAs were used.
RNA libraries were prepared to be compatible with Illumina small RNA sequencing.
We prepared 3′-seq libraries as follows: total RNAs was extracted with TRIzol (Invitrogen). For each sample, poly(A) RNAs were isolated from 10 ug total RNAs, and proceeded with RNA fragmentation, 5′ RNA phosphorylation, and 5′ RNA ligation. After heat denaturation at 65C for 2 min, 5′ adapter-ligated poly(A)-containing RNA fragments were reverse transcribed by superscript II enzyme (Invitrogen) using RT primer ( CPS_RTP: 5′ - GTTCAGAGTTCTACAGTCCGACGATC NNNNNNNNT8VN-3′) at 50 C for 1hr. CPS_RTP was designed to anneal to the junction of 3′ cleaved site and poly(A) tail using its short oligo dT residues and two degenerate nucleotides, and also to contain UMI barcode and adaptor for PCR deduplication, and universal PCR amplification, respectively. The resulting cDNA molecules were amplified by PCR, followed by gel purification of 200 to 500 bp PCR products on 6% PAGE gel in TBE buffer. The eluted PCR products proceed with sequencing on Illumina Nextseq 500.


title: Vav-cre-Tcf7KO-DN1_BC_23

tag: tissue

tag: age

value: 6~8 wks


title: DIPGIV_NKO_c3p5_Input

tag: material

tag: histone mark/factor

value: NKO


title: DIPG36_KO_c3S2p6_Input

tag: crispr

tag: clone or passage


title: Group4-9-m


title: Vav-cre-Tcf7KO-DN1_BC_22

tag: cell type


title: MAC_PROseq_LPS 0h_rep1

description: processed data: PROseq_rep1.txt

tag: cell state

tag: cell line

value: THP-1 monocyte cells were differentiated into macrophage-like cells by PMA for 24 h.


title: Brunello_ACE2 293T-GFP floxed_VSVG_Cre_High_S4

city: Brookings

first: Adam

middle: D.

last: Hoppe

state: South Dakota

address: 1055 CAMPANILE AVE BOX 2202, Avera Health and Science

department: Chemistry and Biochemistry

institute: South Dakota State University

data_processing:
Sequencing reads were aligned to the Brunello library file and counted using MAGeCK 0.5.9.4.
Assembly: Brunello library
Supplementary files format and content: All the raw read count files from MAGeCK were combined into a single .txt file called “Count.files.txt”
Library strategy: CRISPR screen

source_name: cell line

growth_protocol: HEK293T cells were cultured in DMEM suppelemented with 10% FBS and 1% Penicillin/Streptomycin at 37C in 5% CO2 incubator.

extract_protocol:
The genomic DNA was extracted from the sorted cells using Thermo scientific GeneJet Genomic DNA purification kit (Catalogue# K0721). Following extraction of genomic DNA, sgRNAs were amplified for seuqencing.
Equal molar amounts PCR gel-purified samples were pooled, denatured and diluted to 1.8pM, of which 1.3 ml was sequenced on a NextSeq 550 using a high output 75 cycle sequencing kit (Illumina)

treatment_protocol: The cells were transduced with human CRISPR Brunello lentiviral pooled libraries and selected with Puromycin at 1ug/mL. Following selection, they were treated with different pseudoviruses for 48h. Then the cells were sorted in high and low  GFP fluorescence in FACS.

value: cell line

value: Human embryonic kidney

tag: genotype

value: ACE2 expressing HEK293T_GFP_floxed

tag: treatment

value: VSVG-Cre pseudovirus for 48h


title: Group4-8-m

tag: disease state

tag: sample location

tag: medulloblastoma subgroup


title: DIPGIV_KO_c1p5_Input

value: Cell line

value: Input


title: DIPG21_parental_p28_Input

value: Parental


title: Vav-cre-Tcf7KO-DN1_BC_21


title: Brunello_ACE2 293T-GFP floxed_VSVG_Cre_Low-S3


title: Vav-cre-Tcf7KO-DN1_BC_20


title: BT245_KO_c5p8_H3K27ac


title: Group4-7-m

tag: biospecimen id

tag: research subject id

tag: molecule subtype


title: Group4-6-m

value: Cerebellum/Posterior Fossa,Spinal Cord- Cervical,Spinal Cord- Lumbar/Thecal Sac,Spinal Cord- Thoracic


title: DIPGVI-C30-Rx_cells_ChIP1_H3K27me3-C_1


title: Brunello_ACE2 293T_VSVG_mNeonGreen_High_S7

tag: tissue

value: ACE2 expressing HEK293T

value: VSVG-mNeonGreen pseudovirus for 48h


title: DIPG007p149-Rx_cells_ChIP1_H3K27me3-C_1


title: Brunlleo_ACE2 293T_VSVG_mNeonGreen_Low_S6


title: Group4-4-m

value: Medulloblastoma

value: Cerebellum/Posterior Fossa


title: Brunlleo_ACE2 293T_VSVG_mNeonGreen_Presort_S5


title: DIPG007p149-Rx_cells_ChIP1_H3K27ac_1


title: DIPG007p149-Rx_cells_ChIP1_H3K27me2_1


title: Group4-5-m

value: Ventricles

value: mRNA / poly(A)


title: BT869p21-Rx_cells_ChIP1_H3K27me2_1


title: Vav-cre-Tcf7KO-DN1_BC_19

tag: strain/background

tag: genotype/variation

value: Vav-cre; Tcf7fl/fl

value: thymus

tag: age

value: 6~8 wks


title: Group4-2-m_rec

value: Cerebellum/Posterior Fossa, reccurent tumor


title: Vav-cre-Tcf7KO-DN1_BC_1


title: Brunello_ACE2 293T_Spike_mNeonGreen_High_S4

value: cell line

value: Human embryonic kidney

value: SARS-CoV-2 spike-mNeonGreen pseudovirus for 48h


title: Group4-3-m_rec


title: Brunello_ACE2 293T_Spike_mNeonGreen_Low_S3


title: Vav-cre-Tcf7KO-DN1_BC_18


title: Vav-cre-Tcf7KO-DN1_BC_17


title: Brunello_ACE2 293T-GFP floxed_VSVG_Cre_Presort_S2

value: ACE2 expressing HEK293T_GFP_floxed

value: VSVG-Cre pseudovirus for 48h


title: DIPGIV_NKO_c3p5_H3K27me3

tag: material

value: Cell line

tag: histone mark/factor

tag: crispr

value: NKO


title: Group4-1-m


title: Brunello_ACE2 293T_Spike_mNeonGreen_Presort_S2

tag: cell type

value: ACE2 expressing HEK293T


title: Vav-cre-Tcf7KO-DN1_BC_15


title: Vav-cre-Tcf7KO-DN1_BC_16


title: WNT-6-m

source_name: Medulloblastoma WNT

value: WNT


title: Vav-cre-Tcf7KO-DN1_BC_14


title: DIPGIV_NKO_c3p5_H3K27me2

tag: clone or passage


title: DIPGIV_KO_c1p5_H3K27me2

value: KO


title: Vav-cre-Tcf7KO-DN1_BC_12


title: Vav-cre-Tcf7KO-DN1_BC_13


title: Tumor slow 01

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
All of the subsequent analysis, including quality trimming, was executed using the BioSAILs workflow execution system. Trimmomatic (version 0.36) was used for quality trimming of the raw reads to get rid of low-quality bases, systematic base calling errors, as well sequencing adapter contamination (Bolger et al., 2014). The quality of the sequenced reads pre/post quality trimming was assessed by FastQC and only the reads that passed quality trimming in pairs were retained for downstream analysis (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The quality-trimmed RNA-Seq reads were aligned to the Mus musculus GRCm38 (mm10) genome using HISAT2 (version 2.0.4) (Kim et al., 2015). The conversion and sorting of SAM alignment files for each sequenced sample to BAM format was done by using SAMtools (version 0.1.19) (Li et al., 2009). The BAM alignment files were processed using HTseq-count, using the reference annotation file to produce raw counts for each sample.
Assembly: GRCm38 (mm10)
Supplementary files format and content: raw counts

source_name: Tumor tissue slow growing

growth_protocol: Nuclear Myosin 1 Knock-Out (NM1 KO) cell lines were derived from wild-type mouse embryonic fibroblasts (MEFs) (ATCC® CRL-2752) (NM1 WT) using the CRISPR/Cas9 system (Venit et al., 2020b). Cells were grown in DMEM medium containing 10% fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin (Millipore-Sigma) in a humidified incubator with 5% CO2 at 37 °C. For tumor tissue preparation: A total of 10 female 16-week-old nude mice, 25-35 g in weight, were divided into two groups comprised of 5 mice per group. The mice were injected with NM1 WT and NM1 KO embryonic fibroblasts (0.1 mL, 3 x 106 cells/100 µL in 10 mM PBS, pH 7.4) subcutaneously into the right flank of each nude mouse. Mice were weighed daily and monitored for mobility, respiratory distress, and signs of pain for up to 30 days. A weight loss of more than 20% was deemed to be unacceptable and would lead to early sacrifice of the mouse. The tumor size was measured by caliper in each mouse daily and at the end of 30 days cycle, all mice from each group were euthanized by CO2 exposure and perfused with isotonic PBS followed by rapid removal of tumors.

extract_protocol:
RNA from both tumors and cells were isolated by TRIreagent according to manufacturers' protocol.
Total RNA from 4 replicates of NM1 KO MEFs was extracted with TRI Reagent (Millipore-Sigma) according to the manufacturer’s protocol. For transcriptional profiling of tumor tissues, the biggest (fast-growing tumor, TF), and the smallest (slow growing tumor, TS) tumors were selected for comparison. Each tumor was divided to 4 equal pieces and each piece separately homogenized in TRI Reagent by using the Bead Ruptor 96 Homogenizer (Omni International). The RNA-Seq library was prepared by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with the NextSeq 500/550 sequencing platform (performed at the NYUAD Sequencing Center).

tag: strain

value: balbC nude mouse

value: Tumor tissue slow growing


title: Vav-cre-Tcf7KO-DN1_BC_10


title: DIPG36-p20-Rx_cells_ChIP1_H3K27me3-C_1

value: Parental


title: WT-DN3_BC_9

source_name: thymus DN2&DN3 cells (CD45+Lin-CD4-CD8-CD25+)

value: wild type

value: DN2 & DN3


title: Tumor fast 04

source_name: Tumor tissue fast growing

value: Tumor tissue fast growing


title: SHH-23-m

source_name: Medulloblastoma SHH

value: Medulloblastoma

value: Cerebellum/Posterior Fossa

value: SHH

value: mRNA / poly(A)


title: DIPGIV_NKO_c3p5_H3K27ac


title: Tumor slow 04


title: WNT-1-m

value: Cerebellum/Posterior Fossa,Spinal Cord- Lumbar/Thecal Sac


title: WNT-3-m


title: Vav-cre-Tcf7KO-DN1_BC_11

value: Vav-cre; Tcf7fl/fl

value: thymus

value: 6~8 wks


title: Tumor slow 02


title: WNT-2-m


title: Tumor fast 03


title: WT-DN3_BC_96


title: WNT-5-m

value: Ventricles


title: DIPGIV_KO_c1p5_H3K27me3

value: Cell line


title: Tumor fast 02


title: WNT-4-m

value: WNT


title: WT-DN3_BC_95


title: Tumor fast 01

value: balbC nude mouse


title: Tumor slow 03

value: Tumor tissue slow growing


title: SHH-22-m


title: DIPG36_parental_p20_H3K27me2

value: Parental


title: DIPGIV_KO_c1p5_H3K27ac

value: KO


title: SHH-21-m


title: NM1 KO MEF 04

source_name: Mouse embryonic fibroblast

value: Mouse embryonic fibroblast


title: SHH-20-m


title: DIPG36_KO_c3S2p6_H3K27me3


title: SHH-19-m


title: WT-DN3_BC_93

value: wild type

value: DN2 & DN3


title: NM1 KO MEF 01


title: DIPG36p20-Rx_cells_ChIP1_H3K27ac-N_1


title: DIPG36_KO_c3S2p6_H3K27ac


title: DIPG21p28-Rx_cells_ChIP1_H3K27me3-C_1


title: DIPG36_KO_c3S2p6_H3K27me2


title: NM1 KO MEF 03


title: NM1 KO MEF 02


title: DIPG21_parental_p28_H3K27me2


title: pNSCs2

city: Toronto

first: Gary

last: Bader

state: Ontario

address: 160 College St

department: Molecular Genetics

institute: University of Toronto

description: DropSeq

library_source: transcriptomic single cell

data_processing:
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10), and converted to digital gene expression matrices as per the standard instructions http://mccarrolllab.com/dropseq/.
Assembly: mm10
Supplementary files format and content: Gene expression counts as a tab-separated text file, with genes in rows and cells in columns.

source_name: Primary neurospheres derived from forebrain lateral ventricles

growth_protocol: The neurosphere assay was performed as described previously (Chiasson et al., 1999). In brief, pregnant animals were anesthetized with isoflurane, the uterine horns removed and placed into cold artificial CSF. Embryos were cut out from uterine tissue and decapitated. After opening the skull and peeling back the cortex, the walls of the lateral ventricles were cut out from the forebrain and placed in serum-free media (SFM) for dissociation into single cells through mechanical dissociation. Cells were plated in SFM (made in-house from GIBCO Dulbecco’s modified Eagle’s medium and F12) supplemented with Leukemia Inhibitory Factor (LIF) (10 ng/mL) (recombinant). Cells were plated in 24-well culture plates (Nunclon) in serum-free media with EFH at a density of up to 40 cells per microlitre. Resulting neurospheres were counted after 7–10 days in vitro using stringent size criteria: primitive neurospheres were defined as 50 μm or larger in diameter.

extract_protocol:
Primary neurospheres were dissociated and carried on ice to the Drop-seq facility at Princess Margaret Genomics Centre for single cell capture, cDNA amplification, and sequencing library preparation (Macosko et al., 2015).
Libraries were sequenced on an Illumina NextSeq500 to a depth of 60,000 reads per cell.

tag: genotype


title: WT-DN3_BC_91


title: DIPG21p28-Rx_cells_ChIP1_H3K27ac-N_1


title: SHH-17-m

tag: disease state

value: Medulloblastoma

value: Cerebellum/Posterior Fossa


title: SHH-16-m

tag: sample location

value: SHH

value: mRNA / poly(A)


title: MAC_ActD15min_TEDseq_LPS 2h_rep2

description: processed data: ActD_PASisoforms_summary_rep2.txt

data_processing:
Library strategy: TED-seq
RTA v2 software used for basecalling on NextSeq 500 and HiSeq 4000.
After poly-(A) tail trimming, the reads with the length shorter than 15 nucleotides and mean quality score below 20 were filtered out. After PCR duplicates were removed based on UMI barcode, the remaining sequences were mapped to hg38 whole genome using STAR (2.4.2a).  For spike-in genome mapping, BWA was used.
The mapped reads were represented by their 5' terminal  posistions on the same strand, and converted into BED format.
After identifying which gene a TED-seq read is derived from, we estimated poly(A) tail length by subtracting the distance between the 5' end of a TED-seq read and the cleavage and polyadenylation site of the corresponding gene from 300 nucleotides (insert size). For the transcript isoforms that have TED-seq reads more than 50 within 300 nucleotide window upstream of the cleavage and polyadenylation site, ,ean of  poly(A) tail lengths was used to represent poly(A) tail length distributions for transcripts derived from a transcript isoform.
Genome_build: hg38
Supplementary_files_format_and_content: PROseq_rep1.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: PROseq_rep2.txt: matrix_Normalized PROseq readcounts (RPKM)
Supplementary_files_format_and_content: peaks.txt: matrix_Identification of 3′-seq peak positions  with more than 5 CPM.
Supplementary_files_format_and_content: Readcounts_peak.txt: matrix_Normalized abundance (CPM) per the identified 3′-seq peak positions.
Supplementary_files_format_and_content: PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep1.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: ActD_PASisoforms_summary_rep2.txt: matrix_Mean poly(A) tail length for every de novo PAS isoforms.
Supplementary_files_format_and_content: Integrated_datasets.txt: matrix_Transcription in RPKM, mRNA level in CPM, and mean poly(A) tail length for every transcript isoform for the actinomycin D-untrreated conditions.

source_name: Monocyte-derived macrophage cells

extract_protocol:
After washing the cells with DPBS three times, total RNA was extracted by directly adding TRIzol  to the plate with the adherent cells on it. 5 million cells were used for the construction of PRO-seq libraries. For 3′-seq and TED-seq, 10 ug of total RNAs were used.
RNA libraries were prepared to be compatible with Illumina small RNA sequencing.
We prepared TED-seq libraries as described in Woo et. al. (2018)

tag: cell state

value: Differentiated into macrophage-like state

value: Monocyte

tag: cell line

tag: treatment

value: After PMA-mediated differentiaton, THP-1 cells were treated with Actinomycin D for 15 min, followed by  LPS stimulation for 2 hour.


title: WT-DN3_BC_94

value: thymus

value: 6~8 wks


title: WT-DN3_BC_92


title: WT-DN3_BC_89


title: WT-DN3_BC_8


title: SHH-15-m

tag: medulloblastoma subgroup

tag: biospecimen id

tag: research subject id

tag: molecule subtype


title: WT-DN3_BC_88

tag: strain/background

tag: genotype/variation

tag: tissue

tag: age


title: SHH-12-m


title: Flu+Flu+MRSA 2

city: Pittsbrugh

first: John

last: Alcorn

state: PA

address: 4401 Penn Ave

institute: UPMC Children's Hospital of Pittsburgh

data_processing:
Reads per sample were collected and mapped to the Mouse Ensembl reference genome (GRCm39) using CLC Genomics Workbench (Qiagen).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench (Qiagen).
Assembly: GRCm39
Supplementary files format and content: comma separated value files include RPKM and TPM values for each sample as well as total gene reads

source_name: lung tissue

extract_protocol: Mice were euthanized and lungs were taken. Lung tissue was flash frozen with liquid nitrogen, and total RNA was harvested using the Qiagen miRNeasy Mini Kit (cat#217004). After isolation the samples were sequenced using the Illumina TruSeq Platform.

treatment_protocol: On day 0 mice were given either PBS for the acute group or Influenza (A/X31) for the memory group. 54 days later all mice were given influenza (A/PR/8/34) followed by MRSA (USA300) on day 61.

tag: cell type

value: cells from bulk lung tissue

value: WT C57Bl/6

value: Influenza+Influenza+MRSA


title: Flu+Flu+MRSA 3


title: pNSCs1

description: DropSeq

value: Primary neurospheres derived from forebrain lateral ventricles


title: WT-DN3_BC_85


title: SHH-13-m


title: Acute Flu MRSA 3

value: PBS+Influenza+MRSA


title: Acute Flu MRSA 2


title: SHH-11-m


title: SHH-14-m


title: MAC_ActD15min_TEDseq_LPS 0h_rep2

value: After PMA-mediated differentiaton, THP-1 cells were treated with Actinomycin D for 15 min.


title: Flu+Flu+MRSA 1


title: Acute Flu MRSA 1


title: MAC_ActD15min_TEDseq_LPS 0h_rep1

description: processed data: ActD_PASisoforms_summary_rep1.txt


title: MAC_ActD15min_TEDseq_LPS 1h_rep1

value: After PMA-mediated differentiaton, THP-1 cells were treated with Actinomycin D for 15 min, followed by  LPS stimulation for 1 hour.


title: SHH-10-m

value: Ventricles


title: SHH-18-m

value: Medulloblastoma


title: WT-DN3_BC_90

value: wild type

value: DN2 & DN3


title: WT-DN3_BC_87


title: WT-DN3_BC_83


title: WT-DN3_BC_84


title: MAC_ActD15min_TEDseq_LPS 1h_rep2


title: WT-DN3_BC_86


title: MAC_ActD15min_TEDseq_LPS 2h_rep1


title: SHH-9-c_prog

value: Ventricles,  progressive tumor

value: mRNA / poly(A)


title: WT-DN3_BC_81


title: WT-DN3_BC_82


title: SHH-8-c_08m_1104

value: Cerebellum/Posterior Fossa

value: SHH


title: po_e10

description:
Single-cell RNA-seq
metadata_README.txt

data_processing:
Cell Ranger (v2.2.0) was used with default parameters to demultiplex reads and align sequencing reads to the genome, distinguish cells from background, and obtain gene counts per cell. Alignment was performed using the mm10 reference genome build, coupled with the Ensembl transcriptome (v84).
Cells were filtered based on the following quality control metrics: mitochondrial content (indicative of cell damage), number of genes and number of UMIs, using the R package Seurat v2.3. Thresholds for each sample were set based on the distribution of each metric within the sample, which varies with sequencing coverage and number of cells captured. Cluster markers were called for each mouse sample using the Seurat function FindAllMarkers()
Genome_build: mm10
Supplementary_files_format_and_content: metadata_README.txt: text files containing information on the metadata/markers/barcodes/features and matrix files. *.metadata.tsv: Tab-separated file containing info for each cell. *.markers.tsv: Tab-separated file containing cluster markers called for each mouse sample. *_matrix.mtx, *_features.tsv, *_barcodes.tsv: filtered features, barcodes and expression matrices generated by Cell Ranger. *.bw: bigwig files associated with ChIP-seq samples.

source_name: Hindbrain, fresh tissue

extract_protocol:
Mouse embryonic brain structures were dissected from the gestational timepoints E10.5, E13.5, E16.5 and E18.5. Dissections were performed under a Leica stereoscope with a pair of Moria ultra fine forceps (Fine Science Tools), in a PBS solution. The tissue was transferred into ice cold Leibovitz’s medium, followed by single cell dissociation with the Papain System Dissociation.
The concentration of the single cell suspension was assessed with a Trypan blue count. Approximately 10,000 cells per sample were loaded on the Chromium Single Cell 3’ (10X Genomics) system V3 protocol. GEM-RT, DynaBeads cleanup, PCR amplification and SPRIselect beads cleanup were performed using Chromium Single Cell 3’ Gel Bead kit. Indexed single cell libraries were generated using the Chromium Single Cell 3’ Library kit and the Chromium i7 Multiplex kit

tag: phenotype

value: Normal brain mouse

tag: developmental stage


title: ct_e13

description:
Single-cell RNA-seq
metadata_README.txt

source_name: Forebrain, fresh tissue

tag: strain


title: po_e13

description:
Single-cell RNA-seq
metadata_README.txt

source_name: Pons, fresh tissue


title: SHH-6-m_prog

tag: disease state

value: Cerebellum/Posterior Fossa,  progressive tumor


title: ct_e18

description:
Single-cell RNA-seq
metadata_README.txt


title: WT-DN3_BC_79

value: thymus

value: 6~8 wks


title: SHH-5-m_prog

tag: sample location

value: Cerebellum/Posterior Fossa, progressive tumor


title: ct_e16

description:
Single-cell RNA-seq
metadata_README.txt


title: po_e16

description:
Single-cell RNA-seq
metadata_README.txt


title: SHH-3-m


title: WT-DN3_BC_80


title: SHH-7-c_07m_931


title: WT-DN3_BC_7


title: ct_e10

description:
Single-cell RNA-seq
metadata_README.txt


title: po_e18

description:
Single-cell RNA-seq
metadata_README.txt


title: SHH-2-m_prog

value: Frontal Lobe,  progressive tumor


title: SHH-1-m

value: Cerebellum/ Posterior Fossa


title: Group4-34-m

source_name: Medullobalstoma Group 4

value: Cerebellum/Posterior Fossa,Ventricles


title: SHH-4-m


title: WT-DN3_BC_76


title: WT-DN3_BC_77


title: WT-DN3_BC_78


title: Group4-33-m


title: YN, Embryo 6, ICM

city: PALAISEAU

first: Emilie

last: Derisoud

state: Essonne

address: 26 Rue des Prés,

country: France

institute: INRAE

data_processing:
Demultiplexing has been done with bcl2fastq2 version 2.2.18.12 (Illumina) and adapters were trimmed with Cutadapt version 1.15, only reads longer than 10pb were kept.
A de novo assembly was made using StringTie version 2.1.2 following manufacturer instructions to identify XIST in equine embryo samples. The GTF output was aligned on Ensembl 99 EquCab3.0 assembly using IGV version 2.7.2. As XIST position and length on X chromosome was knew (thanks to Pablo Ross) and as XIST is annotated in human, the more similar contig was selected. Y chromosome is not assembly in the EquCab3.0 assembly but a nucleotide sequence of SRY is available on NCBI website.   Both sequences were added to FASTA file from Ensembl 99 EquCab3.0 assembly. Both genes were added to GTF from Ensembl 99 EquCab3.0 assembly as both unique chromosome with one gene composed of one transcript.
STAR version 2.6 was used for the alignment (2-pass mapping with GTF file using parameters: --alignSoftClipAtReferenceEnds No --alignEndsType EndToEnd --alignIntronMax 86545 --alignMatesGapMax 86545) on previously modified Ensembl 99 EquCab3.0 assembly. Genes were then counted with featureCounts from Subreads package version 1.6.1 (parameters: -p -B -C -M).
Genome_build: Ensembl 99 EquCab3.0 assembly + de novo XIST sequence + SRY sequence from NCBI
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Equus caballus

source_name: Blastocyst

growth_protocol: Saddlebred mares (French Anglo-Arabian and Selle Français breeds) were included in this study. They were raised in the “Institut Français du Cheval et de l’Equitation” experimental farm (Chamberet, France, 45° 34’55.17”N, 1°43’16.29”E, 442m). During the protocol period, mares were managed in herds in natural pastures 24h/day with free access to water. The experiments took place from April, the 1st until May 23rd, 2019. All mares remained healthy during this period. The mares’ estrus period was monitored by ultrasound with a 5MHz trans-rectal transducer. During estrus, ovulation was induced with a single 750-1500 IU IV injection of human chorionic gonadotropin (Chrorulon® 5000, MSD Santé animale) as soon as one ovarian follicle >35mm in diameter together with marked uterine edema were observed. At the same time, mares were artificially inseminated with fresh or refrigerated semen containing at least 1 billion motile spermatozoids from a single fertile stallion. Ovulation was confirmed within the next 48 hours by ultrasonography. Embryos were collected 10 days after the insemination (i.e., 8±0.5 days post-ovulation) by non-surgical uterine lavage using prewarmed (37°C) lactated Ringer’s solution (B.Braun) and EZ-Way Filter (IMV Technologies). All embryos were expanded blastocysts grade I or II according to the embryo classification of McKinnon and Squires. They were washed 4 times in commercially available Embryo holding medium (IMV Technologies) and then cut with a microscalpel under binocular magnifying glass to separate pure trophoblast (TE) and inner cell mass enriched hemi-embryo (ICM).

extract_protocol:
Each hemi-embryo was transferred to a DNA LoBind tube (Eppendorf) with extraction buffer from PicoPure RNA isolation kit (Applied Biosystems) and incubated for 30min at 42°C prior to storage at -80°C. The extraction of hemi-embryos RNA was performed using the PicoPure RNA isolation kit (Applied Biosystems), including a DNAse treatment, following the manufacturer’s instructions. RNA quality and quantity were obtained with 2100 bioanalyzer system using RNA 6000 Pico or nano kit (Agilent Technologies) according to the manufacturer's instructions. The RNA Integrity Number median was 9.6 (range from 9.0 to 9.9).
Five nanograms of total RNA (except YN_E1 for which only 2.5ng were used) were mixed with ERCC spike-in mix (Thermofisher) according to the manufacturer recommendations and then used for re-transcription and amplification using the SMART-Seq V4 ultra low input RNA kit (Clontech) according to the manufacturer recommendations. Nine PCR cycles were performed for each hemi-embryo. cDNA quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent Technologies). Libraries were prepared from 0.15 ng cDNA using the Nextera XT Illumina library preparation kit (Illumina). Libraries were pooled in equimolar proportions and sequenced (Paired-end 50-34 pb) on NextSeq500 instrument, using a NextSeq 500 High Output 75 cycles kit (Illumina).

value: Inner Cell Mass

tag: maternal age

tag: maternal parity

tag: embryo size

tag: embryo sex

value: male


title: YN, Embryo 5, TE

value: Trophoblast

value: female


title: YN, Embryo 6, TE


title: WT-DN3_BC_75

value: wild type

value: DN2 & DN3


title: WT-DN3_BC_74


title: Group4-32-m

value: Medulloblastoma

tag: medulloblastoma subgroup

tag: biospecimen id

value: mRNA / poly(A)


title: YN, Embryo 5, ICM


title: WT-DN3_BC_73


title: Group4-31-m_rec

tag: research subject id

tag: molecule subtype


title: YN, Embryo 4, TE


title: YN, Embryo 4, ICM


title: WT-DN3_BC_70

tag: strain/background

tag: genotype/variation


title: Group4-30-m

value: Cerebellum/Posterior Fossa


title: WT-DN3_BC_72

tag: tissue

tag: age


title: WT-DN3_BC_71

tag: cell type


title: Group4-29-m


title: YN, Embryo 3, TE


title: CB-86-c

source_name: Cerebellum Normal

value: normal

value: Amsbio/BioChain _Human normal Cerebellum RNA, Male 24 Y

value: CB

value: circRNA / (poly(A-) / RNaseR+)


title: YN, Embryo 3, ICM


title: WT-DN3_BC_6

value: thymus

value: 6~8 wks


title: WT-DN3_BC_69


title: YN, Embryo 2, TE


title: CB-84-c

value: Takara _Human normal Cerebellum RNA, Pool from 3 Asian Males 21-29 Y


title: WT-DN3_BC_68


title: CB-85-c

value: Amsbio/BioChain _Human normal Cerebellum RNA, Male 29 Y


title: CB-83-c

value: Amsbio_Human brain cerebellum (left), Total RNA, Male 24 Y


title: YN, Embryo 1, TE

value: male


title: YN, Embryo 2, ICM

value: Inner Cell Mass


title: Group4-28-m


title: YN, Embryo 1, ICM


title: WT-DN3_BC_66


title: RB-CR164_S3 - IgG CUT&RUN replicate 1

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
Library strategy: CUT&RUN
Reads were aligned to the mm9 and mm10 builds of the mouse genome using bowtie v2.4.1.
PCR duplicates were removed using samtools v1.10
Contaminating reads mapping to chr11:32270389-32273090 (mm10) were removed
BigWig files were generated from genome coverage using DeepTools 3.4.3 and a scaling factor of 1000/[number of reads mapped to eColi genome]
Genome_build: mm9, mm10
Supplementary_files_format_and_content: BigWig

source_name: Primary haematopoietic/erythroid progenitor cells

growth_protocol: Primary erythroid progenitor cells were isolated from fetal livers, which were freshly isolated at e12.5-e13.5 from C57BL/6 mouse embryos. 5-15 livers were pooled together for each experimental replicate, mechanically dissociated in staining buffer (PBS, 0.2% BSA, 5 mM Glucose) and strained through a 30-um strainer. Cells were immunostained at 4 °C in the presence of rabbit IgG (200 ug/ml, Jackson Laboratories 015-000-003) to block Fc receptors. To enrich for early erythroid progenitors, cells were first stained with 5 ug/ml biotin-conjugated anti-Ter119 (BD 553672) for 30 min, before magnetic depletion using streptavidin nanobeads (BioLegend Mojosort 480016) following the manufacturer’s instructions. Cells were then incubated with 0.5 ug/ml APC-conjugated streptavidin (BD 553672), 0.33 ug/ml PE-Cy7-conjugated anti-CD71 (BioLegend 113811) and a panel of 5 FITC-conjugated lineage antibodies (anti-CD41, anti-CD45R, anti-CD3e, anti-CD11b and anti-Ly-6G/6C, all at 1 ug/ml; BD 553848, 553087, 553061, 557396, and 553126, respectively) for 45 min. Cells were then resuspended in FACS running buffer (staining buffer plus 2 mM EDTA). 0.66 ug/ml Hoechst was added immediately prior to sorting in order to distinguish live cells. Cells were sorted into Eppendorf tubes containing 500 ul RPMI supplemented with 10% FCS using a BD FACSAria Fusion machine with a 100 uM nozzle size.

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul Rabbit IgG antibody (Millipore; 12-370)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.

tag: developmental stage

value: Primary erythroid progenitor cells isolated from fetal liver

tag: immunophenotype

value: Lin- CD71:high Ter119:high

tag: antibody

value: IgG


title: Group3-17-c

source_name: Medullobalstoma Group 3

tag: disease state

value: Medulloblastoma

tag: sample location


title: Group3-14-c


title: RB-CR163_S3 - Gata2 CUT&RUN replicate 1

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul anti-Gata2 Rabbit polyclonal antibody (aG2; kind gift of Emery Bresnick)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.

tag: strain


title: WT-DN3_BC_64

value: wild type

value: DN2 & DN3


title: RB-CR162_S2 - Gata2 CUT&RUN replicate 1

value: Lin- CD71:high Ter119:med


title: WT-DN3_BC_62


title: WT-DN3_BC_63


title: WT-DN3_BC_61


title: Group3-12-c

value: Cerebellum/Posterior Fossa


title: Group3-13-c

value: Ventricles


title: Group3-11-c

value: Cerebellum/Posterior Fossa,Spinal Cord- Cervical,Spinal Cord- Lumbar/Thecal Sac,Spinal Cord- Thoracic

value: circRNA / (poly(A-) / RNaseR+)


title: WT-DN3_BC_67

value: thymus

value: 6~8 wks


title: RBCR196_S0 CD71 medium - Gata2 CUT&RUN replicate 2

value: Lin- CD71:med Ter119-


title: RB-CR161_S1 - Gata2 CUT&RUN replicate 1

value: Lin- CD71:high Ter119-


title: WT-DN3_BC_59


title: Group3-9-c_rec

value: Cerebellum/Posterior Fossa, reccurent tumor


title: RBCR197_S1 - Gata2 CUT&RUN replicate 2


title: WT-DN3_BC_5


title: WT-DN3_BC_60


title: RBCR195_S0 CD71 low - Gata2 CUT&RUN replicate 2

value: Lin- CD71- Ter119-


title: RB-CR160_S0 CD71 medium - Gata2 CUT&RUN replicate 1

value: Primary erythroid progenitor cells isolated from fetal liver


title: Group3-10-c

value: Cerebellum/Posterior Fossa,Ventricles


title: Group3-16-c


title: RRBS mat del mESC day 2.5 diff line 1

city: Parkville

first: Natalia

last: Benetti

state: Victoria

address: 1G Royal Parade

country: Australia

institute: WEHI

description: male

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
adapter trimming of Fastq files using TimGalore! v0.4.4 with Cutadapt v1.15
trimming of the diversity bases introduced by library preparation with the NuGEN Ovation RRBS methyl-seq kit was carried out using the trimRRBSdiversityAdaptCustomers.py script provided by NuGEN
Reads were mapped to the GRCm38.p6 version of the mouse reference genome using Bismark v0.20.0
methylation calls were extracted using Bismark’s bismark_methylation_extractor function
% methylation was calculated using Seqmonk’s Bisulphite methylation over features pipeline, filtering probes with over 10 reads for all libraries
Assembly: GRCm38.p6
Supplementary files format and content: benetti_ESC_RRBS_diff_%me_over_all_CpG_islands.txt: tab-delimited text file containing % methylation values for all CpG islands genome-wide with over 10 reads in each library (blank cells are CpG islands with <10 reads in at least one library)
Supplementary files format and content: benetti_ESC_RRBS_diff_%me_over_Hox_CpG_islands.txt: tab-delimited text file containing % methylation values for all CpG islands within each Hox cluster with over 10 reads in each library (blank cells are CpG islands with <10 reads in at least one library)

source_name: primary mouse embryonic stem cell line

growth_protocol: mESCs derived, and cultured as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z

extract_protocol:
100ng total DNA extracted with Quick-DNA Miniprep Kit (Zymo) then used as library prep input
QIAGEN EpiTect Fast DNA Bisulfite Kit
NuGEN Ovation RRBS methyl-seq system (Integrated sciences)

treatment_protocol: mESCSs were differentiated into NMPs as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z

tag: cell line

value: primary mouse embryonic stem cell line

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors

tag: genotype

value: Smchd1[del/+] (maternally deleted)

tag: time

value: day 2.5 differentation


title: RRBS mat del mESC day 2.5 diff line 2

description: male


title: WT-DN3_BC_65

value: wild type

value: DN2 & DN3


title: RRBS mat del mESC day 2 diff line 2

description: male

value: day 2 differentation


title: WT-DN3_BC_58


title: RRBS mat del mESC day 2 diff line 1

description: male


title: RB-CR159_S0 CD71 low - Gata2 CUT&RUN replicate 1


title: Group3-6-c

value: Medulloblastoma

value: Cerebellum/Posterior Fossa

tag: medulloblastoma subgroup

tag: biospecimen id


title: Group3-5-c

tag: research subject id

tag: molecule subtype

value: circRNA / (poly(A-) / RNaseR+)


title: WT-DN3_BC_57

tag: strain/background

tag: genotype/variation

value: thymus

value: 6~8 wks


title: RBCR198_Lin+ - Gata2 CUT&RUN replicate 2

tag: tissue

value: Lin+ CD71- Ter119-


title: Group4-26-c


title: RRBS wt mESC day 2.5 diff line 2

description: male

tag: cell type

value: Smchd1[fl/+] (wild-type)


title: Group4-27-c


title: WT-DN3_BC_54

tag: age


title: RB-CR81_S4 - Gata1 CUT&RUN replicate 2

data_processing:
Library strategy: CUT&RUN
Reads were aligned to the mm9 and mm10 builds of the mouse genome using bowtie v2.4.1.
PCR duplicates were removed using samtools v1.10
BigWig files were generated from genome coverage using DeepTools 3.4.3 and a scaling factor of 1000/[number of reads mapped to eColi genome]
Genome_build: mm9, mm10
Supplementary_files_format_and_content: BigWig

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul anti-Gata1 Rabbit polycolonal antibody (Abcam; ab11852)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.

tag: developmental stage

tag: immunophenotype

value: Lin- CD71:med Ter119:high


title: WT-DN3_BC_55


title: Group4-25-c

tag: disease state

value: Cerebellum/Posterior Fossa,Spinal Cord- Cervical,Spinal Cord- Lumbar/Thecal Sac,Spinal Cord- Thoracic


title: RB-CR70_S4 - Gata1 CUT&RUN replicate 1

value: Primary erythroid progenitor cells isolated from fetal liver

tag: antibody


title: WT-DN3_BC_53


title: WT-DN3_BC_56


title: RRBS wt mESC day 2 diff line 1

description: male

value: primary mouse embryonic stem cell line


title: RRBS wt mESC day 2.5 diff line 1

description: male

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors


title: RRBS wt mESC day 2 diff line 2

description: male


title: RB-CR77_S3 - Gata1 CUT&RUN replicate 2

value: Lin- CD71:high Ter119:high

tag: strain


title: RB-CR79_S3 - IgG CUT&RUN replicate 2

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul Rabbit IgG antibody (Millipore; 12-370)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.

value: IgG


title: WT-DN3_BC_52

value: wild type


title: WT-DN3_BC_51

value: DN2 & DN3


title: Group4-23-c

extract_protocol:
The medulloblastoma tumor RNA samples were provided by the Childhood Brain Tumor Tissue Consortium (www.cbttc.org), and 5 normal cerebellum RNA samples were purchased commercially from Takara (Japan), Amsbio (UK) or BioChain (USA).
mRNA / poly(A) enriched fraction: ≈ 100 ng of total RNA was used to generate stranded mRNA libraries with the TruSeq®Stranded mRNA Low Throughput Sample Preparation kit according to the manufacturer’s instructions (15031047, Illumina, USA). This protocol involves a poly(A) selection/enrichment and ribosomal RNA depletion step.
circRNA / (poly(A-) / RNaseR+)  fraction: 1 μg of total RNA was used. First, ribosomal RNA was depleted using the RiboMinusTM Eukaryote System V2 (Ambion) (A15026, ThermoFisher USA), followed by digestion with 5U RNase R for 1 hr to degrade linear RNAs and purification with the RNeasy MinElute Cleanup Kit (74204, Qiagen). The concentration and quality of the enriched circRNA RiboMinus/RNase R preparations were assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). 1 ng of RiboMinus/RNase R treated RNA was used for cDNA library generation. Random hexamer primers and Superscript III reverse transcriptase (18080055, Invitrogen, USA) were used for 1st strand synthesis and stranded mRNA library was generated according to the TruSeq®Stranded mRNA Low Throughput Sample Preparation protocol (15031047, Illumina, USA). The concentration and quality of the cDNA libraries were assessed with Qubit (Life Technologies, USA) and TapeStation, respectively.

tag: sample location


title: WT-DN3_BC_50

extract_protocol:
Single-cell cDNA amplification was carried out by using the STRT protocol with several modifications to allow for multiplexed single-cell RNA-seq. Libraries were prepared using KAPA Hyper Prep Kits (KK8505). The NEB U-shaped adapter was used for ligation. The libraries were sequenced on an Illumina Hiseq x ten platform to generate 150-bp paired-end reads (sequenced by BGI).
Libraries are constructed according to the standard protocol for Smart-seq2.


title: Group4-21-c


title: RB-CR78_S3 - Gata1 CUT&RUN replicate 2


title: Group4-22-c


title: Group4-19-c


title: RB-CR158_Lin+ - Gata2 CUT&RUN replicate 1


title: Group4-20-c


title: RB-CR67_S3 - Gata1 CUT&RUN replicate 1


title: RB-CR66_S2 - Gata1 CUT&RUN replicate 1

value: Lin- CD71:high Ter119:med


title: WT-DN3_BC_4


title: WT-DN3_BC_48


title: RB-CR69_S3 - Gata1 CUT&RUN replicate 1


title: RB-CR75_S1 - IgG CUT&RUN replicate 2

value: Lin- CD71:high Ter119-


title: RB-CR65_S1 - Gata1 CUT&RUN replicate 1


title: WT-DN3_BC_47


title: RB-CR74_S1 - Gata1 CUT&RUN replicate 2


title: Group4-24-c

value: Medulloblastoma

value: Cerebellum/Posterior Fossa


title: WT-DN3_BC_46

value: thymus


title: WT-DN3_BC_45

value: 6~8 wks


title: RB-CR73_S0 CD71 medium - Gata1 CUT&RUN replicate 2

value: Lin- CD71:med Ter119-


title: RB-CR64_S0 CD71 medium - Gata1 CUT&RUN replicate 1


title: WT-DN3_BC_44


title: Group4-15-c

value: circRNA / (poly(A-) / RNaseR+)


title: Group4-13-c


title: WT-DN3_BC_49


title: Group4-18-c

value: Ventricles


title: RB-CR63_S0 CD71 low - Gata1 CUT&RUN replicate 1

value: Lin- CD71- Ter119-


title: Group4-14-c


title: WT-DN3_BC_42


title: Group4-12-c


title: RB-CR72_S0 CD71 low - Gata1 CUT&RUN replicate 2

value: Primary erythroid progenitor cells isolated from fetal liver


title: Group4-17-c


title: Group4-16-c


title: WT-DN3_BC_41


title: Group4-11-c


title: RB-CR71_Lin+ - Gata1 CUT&RUN replicate 2

value: Lin+ CD71- Ter119-


title: Group4-10-c


title: KO proB cells rep2_511

city: Badalona

first: Maribel

last: Parra

state: Barcelona

address: Ctra. de Can Ruti, Camí de les Escoles, s/n

department: Lymphocyte Development and Disease

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Quality control of the samples was performed with the FASTQC tool
Resulting bam files were analyzed with Bioconductor package metaseqR and subjected to differential expression analysis
Paired-end reads from RNA-Seq were aligned to the murine reference genome (GRCm38) using Hisat2 (version 2.0.5). Quality of the alignments was assessed using FastQC (v0.11.2).
A count table file indicating the number of reads per gene in each sample was generated using HTSeq (version 0.6.0). Genes with no or very low expression were filtered out.
Genome_build: Genome Reference Consortium Mouse Build 38 (GRCm38-mm10)
Differentially expressed genes were identified using DESeq, requiring a minimum adjusted p-value of 0.05 and a |log2FC| value greater than 1.
Supplementary_files_format_and_content: counts text files

source_name: Primary murine cells

growth_protocol: Cells were extracted from fresh murine bone marrow and sorted to obtain purified pro-B and pre-B cells.

extract_protocol:
Total RNA was extracted at IRB Genomics Unit (Barcelona).
low input library was performed in all samples.
Paired-end mode with 100bp read length. 50 milion paired-end reads were generated per each sample

treatment_protocol: HDAC7 knockout cells have a floxed Hdac7 and a CRE recombinase activated depending on Mb-1 gene promotor.

value: pro-B lymphocytes

tag: genotype

value: HDAC7 Knockout


title: Group4-9-c


title: WT-DN3_BC_40

source_name: thymus DN2&DN3 cells (CD45+Lin-CD4-CD8-CD25+)


title: RB-CR62_Lin+ - Gata1 CUT&RUN replicate 1


title: WT-DN3_BC_3


title: Group4-8-c


title: WT-DN3_BC_39


title: WT proB cells rep2_510

value: wild-type


title: Group4-7-c


title: WT-DN3_BC_43

value: wild type


title: Group4-6-c

value: Cerebellum/Posterior Fossa,Spinal Cord- Cervical,Spinal Cord- Lumbar/Thecal Sac,Spinal Cord- Thoracic


title: KO proB cells rep1_509


title: WT proB cells rep1_508


title: WT-DN3_BC_38

value: DN2 & DN3


title: Group4-5-c


title: WT-DN3_BC_37


title: KO preB cells rep2_507

value: pre-B lymphocytes


title: WT-DN3_BC_36


title: WT-DN3_BC_34


title: WT-DN3_BC_35


title: WT preB cells rep2_506


title: KO preB cells rep1_505


title: Group4-3-c_rec

value: Medulloblastoma

value: Cerebellum/Posterior Fossa, reccurent tumor


title: scRNA-Seq of uterus2: adult female cynomolgus monkey

city: Nanjing

first: Dijun

last: Chen

state: Jiangsu

address: Xianlin

department: Life Sciences

institute: Nanjing University

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines (v3.1.0,10X Genomics).
Genome_build: macFas6
Supplementary_files_format_and_content: barcodes.tsv; features.tsv; matrix.mtx; peaks.bed

organism: Macaca fascicularis

source_name: Uterus

extract_protocol:
The cynomolgus monkey project included 20 RNA and 8 ATAC organs.
RNA: 3' transcriptome sequencing, cDNA fragmentation, end filling, adding A, connection connector, Index PCR

value: Uterus

tag: condition

value: Normal

tag: Sex

value: female


title: WT-DN3_BC_32

value: thymus

value: 6~8 wks


title: WT-DN3_BC_33


title: Group4-2-c_rec

data_processing:
Basecalling and demultiplexing were performed using bcl2fastq (v2.20.0).
Quality and adapter trimming of reads were performed using TrimGalore (v0.6.4).
standard mRNA detection: reads from the poly(A) enriched fraction were aligned to the Gencode GRCh38 reference genome assembly using the Star (v2.5.2) aligner. Counts were assigned to genes using featureCounts (v1.5.1)
circRNA detection: reads from the circRNA enriched fraction were analysed with the CIRCexplorer2 characterization pipeline to identify circular back spliced junctions and aligned to Gencode GRCh38 using CIRCexplorer2/Star (PMID: 27365365) with the default parameters.
linear back spliced transcript detection: reads from poly(A) enriched fraction were analysed with the CIRCexplorer2 characterization pipeline to identify linear back spliced junctions and aligned to Gencode GRCh38 using CIRCexplorer2/Star (PMID: 27365365) with the default parameters.
Fusion detections: reads from the poly(A) enriched fraction and circRNA enriched fraction were aligned to Gencode GRCh38 using Star-Fusion (PMID: 31639029) with the default parameters.
Normalized counts were generated using DESeq2 (v1.32.0).
Assembly: GRCh38
Supplementary files format and content: tab delimited text file with raw mRNA counts for every sample generated by featureCounts
Supplementary files format and content: tab delimited text file with raw circRNA counts for every sample generated by CIRCexplorer2
Supplementary files format and content: tab delimited text file with raw fusion transcript counts for every sample generated by StarFusion

tag: medulloblastoma subgroup

tag: biospecimen id

value: circRNA / (poly(A-) / RNaseR+)


title: WNT-6-c

source_name: Medulloblastoma WNT

value: Cerebellum/Posterior Fossa

value: WNT

tag: research subject id

tag: molecule subtype


title: Group4-4-c


title: WT preB cells rep1_504


title: Group4-1-c


title: WT-DN3_BC_31

data_processing:
Unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails.
Next, we removed reads with adapter contaminants and low-quality bases (N>10%).
The cleaned reads were aligned to the mm10 mouse transcriptome (Genocode) using Tophat (version 2.1.1).
Uniquely mapped reads were counted using htseq-count of the HTSeq package. For each gene, duplicated transcripts with the same UMI sequence were removed. For each cell, the transcript copy number of each gene were counted on the basis of the number of distinct UMIs of that gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcode_information.xlsx
Supplementary_files_format_and_content: count_matrix.csv
Supplementary_files_format_and_content: expression_matrix_log2(TPM:10+1).csv

tag: strain/background

tag: genotype/variation


title: WNT-5-c

value: Ventricles


title: RNAseq reciprocal cross wt mESC day 3 diff line 3

description: male

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and log2-transformed RPKM counts were calculated for each gene using Seqmonk's RNAseq pipeline.
Assembly: GRCm38.p6
Supplementary files format and content: benetti_ESC_RNAseq_reciprocal_cross_log2RPKM_Hox.txt: tab-delimited text file containing log2-transformed RPKM counts normalized by sequencing depth for all Hox genes. Transcript isoforms were merged.
Supplementary files format and content: benetti_ESC_RNAseq_reciprocal_cross_log2RPKM_diff_factors.txt: tab-delimited text file containing log2-transformed RPKM counts normalized by sequencing depth for a list of pluripotency and differentiation factors relevant to mESC to NMP differentiation. Transcript isoforms were merged.
Supplementary files format and content: benetti_ESC_RNAseq_reciprocal_cross_raw_counts_all_genes.txt: tab-delimited text file of raw read counts over all genes

extract_protocol:
100ng total RNA extracted with Quick-RNA Miniprep Kit (Zymo) then used as library prep input
TruSeq Stranded or non-stranded mRNA kit (Illumina)

tag: cell line

value: primary mouse embryonic stem cell line

tag: cell type

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors

value: Smchd1[fl/+] (wild-type)

tag: time

value: day 3 differentation


title: RNAseq reciprocal cross het mESC day 3 diff line 2

description: male

value: Smchd1[del/+] (heterozygous)


title: RNAseq reciprocal cross het mESC day 3 diff line 3

description: male


title: RNAseq reciprocal cross het mESC day 3 diff line 1

description: male


title: WT-DN3_BC_30

value: wild type

tag: tissue

value: DN2 & DN3

tag: age


title: scRNA-Seq of tongue: adult male cynomolgus monkey

source_name: Tongue

value: Tongue

value: male


title: scRNA-Seq of uterus1: adult female cynomolgus monkey

value: Uterus

value: Normal


title: WNT-4-c

tag: disease state

value: Medulloblastoma


title: scRNA-Seq of testis2: adult male cynomolgus monkey

source_name: Testis

value: Testis


title: scRNA-Seq of trachea: adult male cynomolgus monkey

source_name: Trachea

value: Trachea


title: WT-DN3_BC_29

value: thymus

value: 6~8 wks


title: scRNA-Seq of testis1: adult male cynomolgus monkey


title: RNAseq reciprocal cross het mESC day 2.5 diff line 3

description: male

value: day 2.5 differentation


title: WT-DN3_BC_28


title: WT-DN3_BC_2


title: WNT-2-c

value: Cerebellum/Posterior Fossa

value: WNT

value: circRNA / (poly(A-) / RNaseR+)


title: WNT-1-c

value: Cerebellum/Posterior Fossa,Spinal Cord- Lumbar/Thecal Sac


title: RNAseq reciprocal cross wt mESC day 3 diff line 2

description: male

value: primary mouse embryonic stem cell line

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors

value: Smchd1[fl/+] (wild-type)

value: day 3 differentation


title: RNAseq reciprocal cross wt mESC day 3 diff line 1

description: male


title: RNAseq reciprocal cross het mESC day 2.5 diff line 1

description: male

value: Smchd1[del/+] (heterozygous)


title: RNAseq reciprocal cross het mESC day 2.5 diff line 2

description: male


title: RNAseq reciprocal cross wt mESC day 2.5 diff line 2

description: male


title: scRNA-Seq of lung: adult female cynomolgus monkey

source_name: Lung

value: Lung

value: female


title: WT-DN3_BC_26

value: wild type

value: DN2 & DN3


title: WT-DN3_BC_27


title: scRNA-Seq of spleen: adult male cynomolgus monkey

source_name: Spleen

value: Spleen

value: Normal

value: male


title: WNT-3-c

value: Medulloblastoma


title: RNAseq reciprocal cross wt mESC day 2.5 diff line 3

description: male

value: day 2.5 differentation


title: SHH-23-c

source_name: Medulloblastoma SHH

value: Cerebellum/Posterior Fossa

value: SHH


title: WT-DN3_BC_24

value: thymus

value: 6~8 wks


title: SHH-20-c

value: circRNA / (poly(A-) / RNaseR+)


title: WT-DN3_BC_23


title: WT-DN3_BC_25


title: scRNA-Seq of liver1: adult female cynomolgus monkey

source_name: Liver

value: Liver


title: SHH-21-c


title: SHH-22-c


title: scRNA-Seq of stomach: adult male cynomolgus monkey

source_name: Stomach

value: Stomach


title: RNAseq reciprocal cross wt mESC day 2.5 diff line 1

description: male

value: primary mouse embryonic stem cell line

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors

value: Smchd1[fl/+] (wild-type)


title: scRNA-Seq of muscle: adult male cynomolgus monkey

source_name: Muscle

value: Muscle


title: RNAseq reciprocal cross het mESC day 2 diff line 2

description: male

value: Smchd1[del/+] (heterozygous)

value: day 2 differentation


title: scRNA-Seq of liver2: adult male cynomolgus monkey

value: Normal


title: WT-DN3_BC_20

value: wild type

value: DN2 & DN3


title: scRNA-Seq of heart: adult male cynomolgus monkey

source_name: Heart

value: Heart

value: male


title: SHH-17-c

value: Medulloblastoma

value: Cerebellum/Posterior Fossa

value: SHH


title: SHH-19-c

value: circRNA / (poly(A-) / RNaseR+)


title: SHH-16-c


title: WT-DN3_BC_1

value: thymus

value: 6~8 wks


title: WT-DN3_BC_21


title: RNAseq reciprocal cross het mESC day 2 diff line 3

description: male

value: primary mouse embryonic stem cell line


title: SHH-18-c


title: scRNA-Seq of breast: adult female cynomolgus monkey

source_name: Breast

value: Breast

value: female


title: scRNA-Seq of colon2: adult male cynomolgus monkey

source_name: Colon

value: Colon


title: RNAseq reciprocal cross wt mESC day 2 diff line 2

description: male

source_name: primary mouse embryonic stem cell line

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors

value: Smchd1[fl/+] (wild-type)


title: WT-DN3_BC_17


title: RNAseq reciprocal cross wt mESC day 2 diff line 1

description: male

value: day 2 differentation


title: RNAseq reciprocal cross het mESC DME LIF line 3

description: male

value: Smchd1[del/+] (heterozygous)

value: day 0 differentation


title: scRNA-Seq of bladder: adult male cynomolgus monkey

source_name: Bladder

value: Bladder

value: Normal


title: RNAseq reciprocal cross wt mESC day 2 diff line 3

description: male


title: scRNA-Seq of colon1: adult female cynomolgus monkey


title: RNAseq reciprocal cross het mESC day 2 diff line 1

description: male


title: SHH-11-c

value: Medulloblastoma


title: scRNA-Seq of adipose: adult male cynomolgus monkey

source_name: Adipose

value: Adipose

value: male


title: scRNA-Seq of kidney: adult male cynomolgus monkey

source_name: Kidney

value: Kidney


title: SHH-14-c

value: Cerebellum/Posterior Fossa

value: SHH

value: circRNA / (poly(A-) / RNaseR+)


title: WT-DN3_BC_18

source_name: thymus DN2&DN3 cells (CD45+Lin-CD4-CD8-CD25+)

value: wild type

value: thymus

value: DN2 & DN3

value: 6~8 wks


title: WT-DN3_BC_19


title: WT-DN3_BC_14


title: WT-DN3_BC_22


title: SHH-12-c


title: SHH-7-c


title: scRNA-Seq of aorta: adult male cynomolgus monkey

source_name: Aorta

value: Aorta


title: SHH-13-c


title: WT-DN3_BC_16


title: RNAseq reciprocal cross het mESC DME LIF line 1

description: male

value: primary mouse embryonic stem cell line

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors


title: RNAseq reciprocal cross het mESC DME LIF line 2

description: male

value: Smchd1[del/+] (heterozygous)

value: day 0 differentation


title: SHH-10-c

value: Ventricles


title: scATAC-Seq of uterus: adult female cynomolgus monkey

data_processing:
The scATAC-seq sequencing data are pre-processed by cellranger-atac (v1.2.0) with the count command line. The running parameters are used by default except for “--force-cells=”. The “-- force-cell” is 10000 for liver, lung and colon, 8000 for spleen, and the rest of the organs have no restriction on this parameter.
Genome_build: macFas6
Supplementary_files_format_and_content: barcodes.tsv; features.tsv; matrix.mtx; peaks.bed

source_name: Uterus

extract_protocol:
The cynomolgus monkey project included 20 RNA and 8 ATAC organs.
ATAC: Prepare Sample Index PCR Mix mixture, add SI PCR mix, add SI Index N SA, mix well, add SPRIselect, remove supernatant, add ethanol, remove ethanol, centrifuge.

value: Uterus

value: Normal

value: female


title: WT-DN3_BC_15


title: RNAseq reciprocal cross wt mESC DME LIF line 3

description: male

value: Smchd1[fl/+] (wild-type)


title: SHH-8-c

value: Medulloblastoma

value: Cerebellum/Posterior Fossa


title: SHH-15-c

value: SHH

value: circRNA / (poly(A-) / RNaseR+)


title: SHH-5-c_prog

value: Cerebellum/Posterior Fossa, progressive tumor


title: WT-DN3_BC_13

value: wild type

value: thymus

value: DN2 & DN3


title: WT-DN1_BC_9

source_name: thymus DN1 cells (CD45+Lin-CD4-CD8-CD25-CD44+)

value: 6~8 wks


title: scATAC-Seq of heart: adult female cynomolgus monkey

value: Heart


title: RNAseq reciprocal cross wt mESC DME LIF line 2

description: male

value: primary mouse embryonic stem cell line

value: mouse embryonic stem cells in a differentiation time course to neural mesodermal progenitors


title: WT-DN3_BC_12


title: WT-DN1_BC_96


title: scATAC-Seq of lung: adult female cynomolgus monkey

source_name: Lung

value: Lung


title: RNAseq reciprocal cross wt mESC DME LIF line 1

description: male

value: day 0 differentation


title: WT-DN1_BC_95


title: scATAC-Seq of colon: adult female cynomolgus monkey

value: Colon

value: Normal


title: SHH-6-c_prog

value: Cerebellum/Posterior Fossa,  progressive tumor


title: SHH-1-c

value: Medulloblastoma

value: Cerebellum/ Posterior Fossa


title: scATAC-Seq of liver: adult female cynomolgus monkey_1

value: Liver

value: female


title: scATAC-Seq of liver: adult male cynomolgus monkey_2

value: male


title: ChIPseq_WDR5A-HA_bte1_rep3

first: Yangyang

last: Fan

address: No.5 Yiheyuan Road Haidian District,

institute: Peking University

description: WDR5A-HA-ChIP from bte1 mutant rep3

data_processing:
Illumina bcl-convert v3.7.5 software used for basecalling.
After removing reads with adapter sequences and low quality by fastp, the high-quality reads were mapped to the TAIR10 genome assembly of Arabidopsis thaliana using bowtie2 (version 2.3.3) with default parameters.
Peak calling was performed using MACS2 (version 2.2.5) with the following parameters: --keep-dup 1 --gsize 1.2e8 --qvalue 0.05.
The alignments were converted to bigWig files using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage tool from deepTools2 (version 3.1.3) with parameters “--binSize 5 --normalizeUsing CPM”.
Supplementary_files_format_and_content: peak text files

organism: Arabidopsis thaliana

source_name: total seedlings

extract_protocol:
2 g of 9-day-old seedlings grown on MS medium were collected and cross-linked with 1% formaldehyde for 20 min under vacuum and then ground into a fine powder in liquid nitrogen. Chromatin was isolated and sheared into fragments (200–500 bp) by sonication. The sonicated chromatin was incubated with antibody-bound Sera-Mag SpeedBeads Protein A/G Magnetic Particles (17152104010150, GE Healthcare) overnight at 4℃. Precipitated DNA was then reverse-crosslinked and digested with RNase A and Proteinase K, after which it was purified with the ChIP DNA Clean & Concentrator kit (D5205, Zymo research) according to the manufacturer’s instructions.
All ChIP-seq libraries were generated with the NEBNext® Ultra II DNA Library Prep Kit for Illumina® (E7645S, NEB) according to the manufacturer’s instructions.

value: total seedlings

tag: developmental stage

value: 9-day-old seedlings grown under continuous white light

tag: chip antibody

value: WDR5a-HA (anti-HA Magnetic Beads (88837, Thermo))

value: bte1 mutant


title: SHH-3-c

source_name: Medulloblastoma SHH

tag: sample location

value: Cerebellum/Posterior Fossa

value: SHH

value: circRNA / (poly(A-) / RNaseR+)


title: ChIPseq_WDR5A-HA_bte1_rep2

description: WDR5A-HA-ChIP from bte1 mutant rep2

tag: genotype


title: PFA9_hypox_p3.Input

data_processing:
ChIP-seq datasets were processed using the ChIP-seq module of GenPipes (v3.1.0 for isogenic cell lines, v3.1.2 for parental cell lines). Raw reads were trimmed using Trimmomatic (v0.32) to remove adaptor and sequencing-primer associated reads then aligned to hg19 using bwa-mem (v0.7.12) with default parameters. PCR duplicate reads as defined by reads with identical mapping coordinates were then collapsed by Picard (v2.0.1) to produce uniquely aligned reads. Reads with a mapping quality of 5 or less were then filtered out. For single-end (SE) 50bp datasets, reads were extended by 250bp.
Wiggle tracks are generated using uniquely aligned reads using Homer (v4.9.1). ChIP-seq RPKM values over CGIs and genome-wide 100kb bins for scatterplots were calculated using VisRSeq (v0.9.40).
Rx- and RPKM-normalized BigWig tracks were produced using the “bamCoverage” functionality of deeptools (v3.5.1). Rx ratios were supplied via the ‘--scaleFactor’ option.  Reads flagged as duplicates, mapping to random, mitochondrial or sex chromosomes, as well as low-mappability regions according to ENCODE’s blacklist were discarded.
Assembly: hg19
Supplementary files format and content: bigwig files. Read coverage for each sample over the human genome

source_name: Posterior fossa

extract_protocol:
Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP or HyperPrep Illumina library preparation reagents. Ffor HTP kit, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adapter ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, at 20°C for 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. For HyperPrep kit, end-repair and A tailing were performed in one reaction: 15ul of ChIP sample was incubated with 45ul end repair+A-tailing mix at 20°C for 30 min, then 65°C for 30 min. Directly proceeded to adapter ligation by adding 5ul of IDT for Illumina Unique Dual Indexes (IDT) adapters and 45ul ligation buffer enzyme mix, incubating at 20°C for 15 min, followed by Ampure XP bead purification. Library enrichment: 10 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments.

tag: material

value: cell line

tag: histone mark/factor

value: Input

tag: perturbation

value: Parental


title: H2AK119ub CUT&RUN wt mESC line 3

description: Maternal deletion with Zp3-Cre

data_processing:
Library strategy: CUT&RUN
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth library size using Seqmonk.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt file containing log2-transformed read counts normalized by library size within bins created ±2.5kb centered on a list of MACS peaks determined using SeqMonk's MACS-like functionality for each genotype separately.  MACS peaks were called between H2AK119ub ChIP and input samples from Fursova et al., 2021 (Genes Dev . 2021 May 1;35(9-10):749-770.  doi: 10.1101/gad.347005.120.  Epub 2021 Apr 22) . Peak lists from biological replicates were merged before peak calculation.

source_name: mESC cultured in 2i+LIF medium

extract_protocol:
Fresh cells were subject to CUT&RUN for H2AK119ub. DNA was extracted with phenol/chloroform/isoamyl alcohol
NEBNext Ultra II DNA Library Prep Kit for Illumina
CUT&RUN was performed as described in Skene and Henikoff eLife 2017;6:e21856 DOI: 10.7554/eLife.21856 DNA was purified by phenol/chloroform/isoamylalcohol extraction followed by glycogen/ethanol precipitation
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: development stage

value: Pluripotent state

value: Smchd1[fl/+] (wild-type)

tag: strain

value: C57BL/6/Cast F1

tag: Sex

value: M

value: mESC


title: WT-DN1_BC_93

tag: strain/background

tag: genotype/variation

value: wild type

value: thymus

value: 6~8 wks


title: scATAC-Seq of spleen: adult male cynomolgus monkey

source_name: Spleen

value: Spleen

tag: condition

value: Normal

value: male


title: SHH-4-c

value: Medulloblastoma

value: Cerebellum/Posterior Fossa

tag: medulloblastoma subgroup

tag: biospecimen id

tag: research subject id

tag: molecule subtype


title: SHH-2-c_prog

tag: disease state

value: Frontal Lobe,  progressive tumor

value: circRNA / (poly(A-) / RNaseR+)


title: ChIPseq_WDR5A-HA_bte1_rep1

description: WDR5A-HA-ChIP from bte1 mutant rep1

tag: tissue

value: total seedlings

tag: developmental stage

value: 9-day-old seedlings grown under continuous white light

tag: chip antibody

value: WDR5a-HA (anti-HA Magnetic Beads (88837, Thermo))

value: bte1 mutant


title: H2AK119ub CUT&RUN mat del mESC line 3

description: Maternal deletion with Zp3-Cre

value: Pluripotent state

tag: genotype

value: Smchd1[del/+] (maternally deleted)

value: C57BL/6/Cast F1

tag: cell type


title: WT-DN3_BC_11

value: wild type

value: DN2 & DN3

tag: age


title: WT-DN3_BC_10

value: thymus

value: 6~8 wks


title: WT-DN1_BC_94


title: H2AK119ub CUT&RUN mat del mESC line 1

description: Maternal deletion with Zp3-Cre

tag: development stage

value: M

value: mESC


title: scATAC-Seq of kidney: adult male cynomolgus monkey

value: Kidney

value: Normal

value: male


title: PFA5-Rx-XChIP_K27me2

tag: material

value: cell line

tag: histone mark/factor

tag: perturbation

value: Parental


title: WT-DN1_BC_92

tag: strain/background

tag: genotype/variation


title: H2AK119ub CUT&RUN wt mESC line 2

description: Maternal deletion with Zp3-Cre

value: Smchd1[fl/+] (wild-type)

tag: strain

tag: Sex


title: WT-DN1_BC_91


title: ChIPseq_WDR5A-HA_WT_rep3

description: WDR5A-HA-ChIP from WT rep3

value: total seedlings

value: 9-day-old seedlings grown under continuous white light

value: WDR5a-HA (anti-HA Magnetic Beads (88837, Thermo))

value: Col-0 ecotype


title: WT-DN1_BC_90


title: H2AK119ub CUT&RUN mat del mESC line 2

description: Maternal deletion with Zp3-Cre

value: Pluripotent state

value: Smchd1[del/+] (maternally deleted)

value: C57BL/6/Cast F1


title: H3K27me3 CUT&RUN mat del mESC line 3

description:
Maternal deletion with Zp3-Cre
benetti_CUT_RUN_H3K27me3.txt

data_processing:
Library strategy: CUT&RUN
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth library size using Seqmonk.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt file containing log2-transformed read counts normalized by library size within bins created ±2.5kb centered on a list of MACS peaks determined using SeqMonk's MACS-like functionality for each genotype separately.  MACS peaks were called between H3K27me3 ChIP and input samples from Liu et al., 2016 (Nature . 2016 Sep 22;537(7621):558-562.  doi: 10.1038/nature19362.  Epub 2016 Sep 14.). Peak lists from biological replicates were merged before peak calculation.

extract_protocol:
Fresh cells were subject to CUT&RUN for H3K27me3. DNA was extracted with phenol/chloroform/isoamyl alcohol
NEBNext Ultra II DNA Library Prep Kit for Illumina
CUT&RUN was performed as described in Skene and Henikoff eLife 2017;6:e21856 DOI: 10.7554/eLife.21856 DNA was purified by phenol/chloroform/isoamylalcohol extraction followed by glycogen/ethanol precipitation
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: ChIPseq_WDR5A-HA_WT_rep2

description: WDR5A-HA-ChIP from WT rep2


title: PFA4-Rx-XChIP_K27me2