title: sn_input

data_processing:
Raw reads were trimmed using trim_galore (v0.6.10) and mapped to mouse reference genome (GRcm39) using Bowtie2[54] (V2.5.1) with parameters: -X 2000 -I 10. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. The signal tracks and heatmap were both generated by deepTools[55] (V3.5.2). Given the low-input cells and the nature of oocytes, the histone modification data between two stages were randomly subsampled to an equal number of reads and the broad peaks were called using GoPeaks[56] (V1.0.0) with parameters: --broad --mdist 3000. For ATAC-seq, Genrich (V0.6.1, https://github.com/jsh58/Genrich) was used to identify open genomic regions with parameters: -j -D. Then genome annotation was carried out using ChIPseeker[50] (V1.38.0) with parameters: tssRegion = c(-2000,0) downstream Distance = 0.
Assembly: GRCm39
Supplementary files format and content: bigWig for each sample

extract_protocol:
Briefly, 200 oocytes freed of zona pellucida were incubated with concanavalin-coated magnetic beads (Vazyme, TD904) for 15 minutes at room temperature.
CUT&Tag for H3K4me3 and H3K27me3 were performed following the protocol as previously described[45], with minor adaptations. Briefly, 200 oocytes freed of zona pellucida were incubated with concanavalin-coated magnetic beads (Vazyme, TD904) for 15 minutes at room temperature. This was followed by incubation with 1 μg of either H3K4me3 (Diagenode, C15410003) or H3K27me3 (Diagenode, C15410195) antibody at 4°C overnight, and subsequently with goat anti-rabbit IgG antibody (Vazyme, Ab207) for 1 hour. The samples were incubated with 0.08 μM pA/G-Tnp Pro on a rotator at room temperature for 1 hour, subsequently resuspended in 50 µL of Trueprep Tagment Buffer L, and incubated at 37°C for 1 hour. After tagmentation, DNA extraction was performed using DNA Extract Beads Pro. Finally, the libraries were constructed through 17 cycles of PCR amplification using the TruePrep Index Kit for Illumina (Vazyme, TD202).


title: 8wk_C57-WT_batch-1_sample-p645f

status: Public on Jan 08 2025

type: SRA

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

country: USA

institute: Children's Hospital of Philadelphia

library_source: transcriptomic

data_processing:
read trimming, alignment, read de-duplication, counting, and quantification using nf-core/rnaseq v3.7 with default parameters
differential gene expression testing using DEseq2 v1.38.0 with batch, age, and genotype as factors in the design formula
batch effect regression and heatmap generation using scanpy v.1.8.1
Assembly: GRCm38
Supplementary files format and content: gene_counts_scaled.tsv is a tab separated value file containing scaled counts for each gene in each sample (as quantified in the nf-core/rnaseq pipeline by salmon). It serves as a ‘raw’ counts table suitable for downstream processing with DEseq2 or similar tools.

molecule: polyA RNA

organism: Mus musculus

source_name: lung

extract_protocol:
AT2 cells were isolated by FACS from dissociated primary mouse lung tissue and sorted into trizol for bulk RNA extraction.
poly-A selection was performed on isolated bulk RNA to enrich for mRNA. Subsequently, enriched mRNA was fragmented and Illumina sequencing adapters were ligated before QC and sequencing.

tag: tissue

value: lung

tag: cell type

tag: genotype

tag: batch

tag: age


title: PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl4

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_41_PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl4

library_source: genomic

data_processing:
H3K27me3 CUT&RUN sequencing results were aligned to a concatenated mm10 and dm6 genome using BWA-MEM and normalized to dm6 spike-in reads using CompChIPseq algorithm.  Peaks were called using SICER2 algorithm.
Assembly: mm10
Supplementary files format and content: bed
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

source_name: Patient derived xenograft

extract_protocol:
CUT&RUN was performed according to EpiCypher CUTANA CUT&RUN protocol.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645L). Pooled libraries were sequenced using Novaseq 6000 with a target of 10 million paired end reads per sample.

value: Patient derived xenograft

tag: chip antibody

value: tri-methyl-histone H3 (Lys27) (C36B11) rabbit mAb (Cell Signaling #9733)

value: t(14;18) translocation; EZH2Y641F

tag: treatment

value: Vehicle PO, BID for 14 days


title: 18S_G-RF4-T14

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

country: China

institute: Yangzhou University

description: Library name: Sample 22

data_processing:
For the data processing of rumen microbiomes, raw fastq reads were demultiplexed according to sample-specific barcodes and imported to QIIME2 software (version QIIME2-202402)
The poor-quality bases, adapters and specific primers were trimmed, and the sequences were denoised and binned to amplicon sequence variants (ASVs) using the denoise-paired function of DADA2 plugin for QIIME2.
The feature-classifier plugin was used to construct the specific primer classifiers for the protozoa (316F and 539R of the 18S rRNA gene) based on the SILVA database (version 138). The ASVs were then classified taxonomically based on the specific protozoal classifiers.
The align-to-tree-mafft-fasttree function of the phylogeny plugin was used to construct the phylogenetic trees after the filtering the rare ASVs, and the mitochondria and chloroplast reads. The unweighted unifrac distances for ordination and clustering were calculated using the beta-phylogenetic function of the diversity plugin, and the principal coordinate analysis (PCoA) was performed and visualization by the R software (v4.2) package ggplot2 (v3.4.4).
The alpha diversity parameters (Faith-PD, Chao 1, Shannon, and Simpson) were calculated using the alpha or alpha-phylogenetic function of the diversity plugin. The relative abundance of ruminal protozoa at phylum, family, and genus levels were generated using the relative-frequency function of the feature-table plugin.
Assembly: The V4 region of the eukaryotic 18S rRNA gene was amplified with primers 316F (GCTTTCGWTGGTAGTGTATT) and 539R (CTTGCCCTCYAATCGTWCT).
Supplementary files format and content: 18S_feature_table_with_taxonomy.xlsx, 18S-repset-seqs.fasta

organism: Ovis aries

source_name: ruminal fluid

extract_protocol:
Total genomic DNA was isolated from 1 mL of freeze rumen fluid using TIANamp Stool DNA Kit (DP328, Tiangen) according to manufacturer's instruction.
Amplicon sequencing of rumen 18S rRNA sequencing were performed according to Illumina  protocols with all amplicon libraries being sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA) with 250-base-paired end reads.

value: ruminal fluid

value: Grain-diet treatment

tag: time


title: 18S_G-RF4-T10

description: Library name: Sample 21


title: 8wk_C57-WT_batch-1_sample-p645e


title: 18S_G-RF4-T6

description: Library name: Sample 20


title: 48wk_C57-WT_batch-0_sample-p524c


title: nsn_input

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

source_name: oocyte

value: oocyte


title: 48wk_C57-WT_batch-0_sample-p524d


title: PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl2

description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_39_PDX_DLBCL-EZB_vehicle_H3K27me3CnR_rep2


title: h3k4me3_sn_rep2


title: 18S_G-RF4-T2

description: Library name: Sample 19


title: PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl1

description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_38_PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl1


title: h3k4me3_sn_rep1


title: 48wk_C57-WT_batch-0_sample-p523a


title: h3k4me3_nsn_rep2


title: h3k4me3_nsn_rep1


title: 48wk_C57-WT_batch-0_sample-p493b


title: 18S_G-RF3-T18

description: Library name: Sample 17


title: 18S_G-RF3-T22

description: Library name: Sample 18


title: h3k27me3_sn_rep3


title: 8wk_HPS2_batch-2_sample-HPS2.4


title: U87 spheres sgCYP3A5-2

city: Tianjin

first: Wentao

last: Hu

state: Tianjin

address: No. 94, Weijin Road, Nankai District, Tianjin

institute: School of medicine, NANKAI university

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.Then clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. Read counts of each gene were obtained by HTSeq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text file included raw counts for each sample

molecule: total RNA

source_name: glioma stem-like cell

growth_protocol: cells were grown as neurospheres in serum-free media consisting of DMEM/F12, B27 lacking vitamin A (Invitrogen), 2 µg/mL heparin (STEMCELL), 20 ng/mL EGF (R&D), and 20 ng/mL bFGF (R&D).

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA).
RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: glioma stem-like cell

value: CYP3A5 KO


title: PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl5

description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_42_PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl5


title: NSN_rep1

data_processing:
Adaptors and low-quality bases were removed by using trim_galore (v0.6.10) with default parameters from raw reads. Retained reads were mapped to mouse reference genome (GRCm39) by using HISAT2(54) (v2.2.0) with gencode annotation (vM34). Read quantification was carried out with FeatureCounts(55) (v2.0.6) (parameters: -t exon -g gene_id -Q 10 --primary -s 0 -p --countReadPairs) and normalized to fragments per kilobase of transcript per million mapped (FPKM) values using customized script. To determined differential expression genes, DESeq2(56) (V1.40.1) was used with parameters: foldchange ≥ 1.2, padj < 0.05.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
The zona pellucidae of oocytes were removed with 0.5% pronase E (Sigma). 15 oocytes per sample (3 samples for each group) were lysed and subjected to first strand synthesis.
The transcriptome analysis of GV oocytes was conducted via Smart-seq2, following our previously described methodology(49). 15 oocytes were lysed in 0.2% Triton X-100 containing 80 U RNase Inhibitor. First-strand cDNA synthesis involved the Oligo(dT) VN primer, followed by the 5’TS oligo primer. Subsequently, cDNA amplification was carried out using an ISPCR primer in an 18-cycle PCR and the products underwent purification via VAHTS DNA Clean Beads (Vazyme, N411). Quality control for the amplification products involved measuring cDNA concentration with Qubit 4 and assessing cDNA fragment distribution with Qsep 400. Following this, sequencing libraries were prepared with the TruePrep DNA Library Prep Kit for Illumina (Vazyme, TD503).


title: U87 spheres sgCYP3A5-3


title: U87 spheres sgCYP3A5-1


title: 8wk_HPS2_batch-2_sample-HPS2.3


title: h3k27me3_sn_rep2


title: 18S_G-RF3-T14

description: Library name: Sample 16


title: PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl3

description:
EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.
SICER2 peaks
Sample_40_PDX_DLBCL-EZB_vehicle_H3K27me3CnR_repl3


title: U87 spheres sgControl-3

value: WT


title: 18S_G-RF3-T10

description: Library name: Sample 15


title: 18S_G-RF3-T6

description: Library name: Sample 14


title: U87 spheres sgControl-1


title: U87 spheres sgControl-2


title: h3k27me3_nsn_rep3


title: 8wk_HPS2_batch-2_sample-HPS2.1


title: 18S_G-RF3-T2

description: Library name: Sample 13


title: h3k27me3_nsn_rep2


title: 8wk_HPS1_batch-2_sample-HPS1.4


title: 18S_G-RF2-T22

description: Library name: Sample 12


title: h3k27me3_nsn_rep1


title: 8wk_HPS1_batch-2_sample-HPS1.3


title: 18S_G-RF2-T18

description: Library name: Sample 11


title: 8wk_HPS1_batch-2_sample-HPS1.2


title: PBMCs, Figure_2D

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description: Hybridized Probe-based RNA capture on 10x Barcoded Beads. Multiplexed pool with samples: BL05012_2d, BL05044_2d, BL05045_2d, PB04745_2d

library_source: transcriptomic single cell

data_processing:
10x Cell Ranger Pipeline
Scrublet Doublet Detection
Assembly: GRCh38
Supplementary files format and content: H5 cell by gene matrix, csv with doublet information, fcs files represent data for the flow cytometry results shown in our figure 2

source_name: Blood

extract_protocol:
Chromium Fixed RNA Profiling for Multiplexed Samples (CG000527)
PBMC enriched samples were processed according to the 10x Genomics protocol for Fixation of Cells and Nuclei (CG000478, Rev C). Probe hybridization was completed according to the 10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673,  Rev A).
10x Genomics protocol for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev A).
Chromium Fixed RNA Profiling for Multiplexed Samples (CG000527)

value: Blood

tag: library type

value: mRNA


title: sn_rep22

extract_protocol:
Initially, oocytes were cultured in M2 medium containing 2.5 μM milrinone and 5 μg/mL cytochalasin B for 15 minutes. The GV nucleus was precisely extracted with minimal cytoplasmic carryover, utilizing a Piezo impact-driven micromanipulator.
After washing with 0.5% PVA/PBS, 50 nuclei were added to 50 μL of lysis buffer (100 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40 and 0.05% digitonin) for 10 minutes, and then subjected to tagmentation in TTBL mix (TD711, Vazyme) for 0.5 hours at 37°C. 5 μL of stop buffer was added to the reaction tube and incubated for 5 minutes at room temperature. DNA fragments were purified using ATAC DNA extract beads, underwent library amplification for an 18-cycle PCR, and subsequently, the libraries were purified again using 1.2× VAHTS DNA Clean Beads.

tag: group

value: surrounded nucleolus


title: HepG2 cells, K488R

city: Hefei

first: Zetan

last: Jiang

state: Anhui

address: huangshan Road

institute: UCTC

description: sh+R

data_processing:
cufflinks v.2.2.1 were used to analyze RNA-seq data.
Gene differential expression analysis was carried out with the DEGSeq R package (1.26.0).
Assembly: human genome hg19. TopHat2 v.2.1.0
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimitedtext fles include FPKM values for each Sample

source_name: liver

extract_protocol:
RNA was havested using Tizol reagent，RNA integrity was assessed using the Fragment Analyzer 5400 (Agilent  Technologies, CA, USA). Libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB).
RNA libraries were prepared for sequencing using standard lllumina protocols

value: liver

tag: cell line

value: HepG2 cells


title: 18S_G-RF2-T14

description: Library name: Sample 10


title: HepG2 cells, WT

description: sh+WT


title: 8wk_HPS1_batch-2_sample-HPS1.1


title: 18S_G-RF2-T10

description: Library name: Sample 9


title: sn_rep21


title: 8wk_HPS2_batch-2_sample-HPS2.2


title: 18S_G-RF2-T6

description: Library name: Sample 8


title: HepG2 cells, sh

description: sh+EV


title: sn_rep11


title: 8wk_C57-WT_batch-2_sample-C57.4


title: 8wk_C57-WT_batch-2_sample-C57.3


title: h3k27me3_sn_rep1


title: sn_rep12


title: HepG2 cells, NTC

description: NTC+EV

value: NTC


title: 18S_G-RF2-T2

description: Library name: Sample 7


title: DNMT3L_OE_BTS11_3

city: Cambridge

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
*library strategy: post-bisulphite adaptor tagging (PBAT) bisulphite-seq
Trimming using Trim Galore (v0.6.2) was performed to remove adaptors and poor quality bases from the 3' end. In addition 9bp were trimmed from the 5' end to remove PBAT biases
Bismark (v0.23.1) was then used to map to GRCh38, deduplicate and perform the methylation extraction following default parameters for PBAT processing
Assembly: GRCh38
Supplementary files format and content: DNA methylation values are provided for 100-CpG windows with at least 10 informative CpGs, spanning all autosomes.  Data is provided as a text file.

growth_protocol: Two cell lines of hTSCs (BTS11 and CT29) were obtained from the Arima lab upon written request (Okae et al., 2018). BTS refers to cell lines derived from a blastocyst stage embryo whilst CT originates from 1st trimester placental cytotrophoblast cells.  BTS11 and CT29 were initially cultured using the previously described protocol (Okae et al., 2018) with an updated concentration of CHIR99021 to 4µM (Sheridan et al., 2021). Samples were grown in Okae Media (OM) (Okae et al., 2018) or Trophoblast Organoid Media (TOM), detailed below, for 4 weeks. These cells were initially grown in standard 2D conditions until 80% confluent, then technical replicates of each cell line were either maintained in 2D culture conditions or moved into Matrigel for 3D culture. The conversion of 2D cultures into  3D trophoblast organoid was achieved by plating a single cell suspension onto 25µl Matrigel doplets in 48 well plates and culture followed the published protocol (Turco et al., 2018) for a total of 4 passages. During this time, cultures were overlaid with TOM media: Advanced DMEM/F12 (Thermo Fisher Scientific), N2 supplement (Thermo Fisher Scientific, 17502048, B27 supplement minus vitamin A (Thermo Fisher Scientific, 12587010; at manufacturer's recommended concentration), Primocin 100 μg/ml (InvivoGen, ant-pm),N-acetyl-L cysteine 1.25 mM (Sigma-Aldrich, A9165), L-glutamine 2 mM (Sigma-Aldrich, 25030024), recombinant human EGF 50 ng/ml (Peprotech, AF10015), CHIR99021 1.5 μM (Tocris, 4423), recombinant human R-spondin-1 80 ng/ml (R&D systems, 4645-RS-01M/CF), recombinant human FGF-2 100 ng/ml (Peprotech, 100-18B), recombinant human HGF 50 ng/ml (Peprotech, 100-39), A83-01 500 nM (Tocris, 2939), prostaglandin E2 2.5 μM (Sigma-Aldrich, P0409), and Y-27632 2 μM (Millipore, 688000).  After 4 weeks of culture, cells were dissociated at single cell suspension (Sheridan et al., 2020) and counted on a haemocytometer. Aliquots of 5000 cells were frozen in PBS at -80°C before proceeding to the bisulphite-sequencing.

extract_protocol:
Aliquots of 5000 cells suspended in PBS were thawed and then lysed in 10mM Tris buffer with 0.5% SDS and proteinase K at 37°C for 1 hour.
Bisulphite conversion was done using the EZ DNA Methylation Direct Kit (Zymo Research), as per the manufacturers protocol. First and then second strand synthesis was performed on eluted DNA using Klenow Fragment (3’->5’ exo-) enzyme (New England Biolabs) and customised 9bp random sequence containing biotin-conjugated adaptors. Using Phusion High-Fidelity DNA polymerase (New England Biolabs), libraries were amplified for 10 cycles in a 50uL reaction.

treatment_protocol: The BTS11 cell line was transduced with lentiviral particles of either pLV[Exp]-EGFP:T2A:Puro-EF1A>ORF_Stuffer (control) (VectorBuilder VB010000-9389rbj) or pLV[Exp]-EGFP:T2A:Puro-EF1A>hDNMT3L[NM_013369.3] (VectorBuilder VB900013-3690ksg) to overexpress DNMT3L. In both cases, the lentiviral particles were packaged by VectorBuilder. The BTS11 cells were transduced with the lentivirus supplemented with 8 μg/ml polybrene (Millipore, TR-1003-G) for 24 hours. After 48 hours, the cells were selected by adding 1 µg/ml puromycin to the medium for 7 days.

value: Trophoblast stem cells

tag: Sex

value: male

value: 2D culture in okae media in normoxia treated with DNMT3L expressing lentivirus


title: 18S_G-RF1-T22

description: Library name: Sample 6


title: nsn_rep22

value: non-surrounded nucleolus


title: 8wk_C57-WT_batch-2_sample-C57.1

value: lung


title: nsn_rep21


title: 8wk_C57-WT_batch-2_sample-C57.2


title: DNMT3L_OE_BTS11_2


title: nsn_rep12


title: 8wk_HPS1-2_batch-1_sample-X2464


title: 18S_G-RF1-T18

description: Library name: Sample 5

value: ruminal fluid


title: 18S_G-RF1-T14

description: Library name: Sample 4

value: Grain-diet treatment


title: nsn_rep11

value: oocyte


title: PBMCs, Figure_2A,2B,2C

description: Hybridized Probe-based RNA capture on 10x Barcoded Beads. Multiplexed pool with samples: PB00607_2abc, PB00609_2abc, PB00610_2abc


title: 8wk_HPS1-2_batch-1_sample-X2463


title: 18S_G-RF1-T10

description: Library name: Sample 3


title: Germ line control

data_processing:
Sequences were aligned by BWA mem and deduplicated by Sentieon dedup.
Base recalibation was calculated by Sentieon.
Variants were called against the germline using TNScope.
Variants were filtered using snpEff.
Assembly: mm10
Supplementary files format and content: VCF files as compared to the germline

source_name: Tail

growth_protocol: B lymphoma cells isolated from a mesenteric lymph node of a R26BCL2+Ezh2Y641F mouse that developed follicular lymphoma were injected into a Rag1KO mouse via IP(passage 1). Lymphoma cells grown in the Rag1KO recipients were isolated and injected into a new Rag1KO mouse (passage 2). We repeated the passages 6 times and finally obtained a lymphoma cells that can proliferate in vitro and we named the cell line "tFL-P6". To To investigate if the cell line has acquired additional mutations, we extracted gDNA from tFL-P6 grown in a Rag1KO recipient, original lymphoma cells grown in the GEMM (P0), and tail of the GEMM as a germline control,   and perfromed whole genome sequencing.

extract_protocol:
Genomic DNA was isolated using QIAGEN All-prep DNA/RNA extraction kit.
Library prep and whole genome sequence was performed in Medgenome.

value: Tail

value: Normal contropl

value: Human BCL2 and Ezh2Y641F mutation KI


title: BTS11_C2

value: 2D culture in okae media in normoxia treated with control lentivirus


title: 18S_G-RF1-T6

description: Library name: Sample 2


title: 8wk_HPS1-2_batch-1_sample-X2341


title: tFL-P6

source_name: Lymph node

value: Lymph node

value: B cell lymphoma


title: Original tumor (P0)


title: 48wk_HPS1-2_batch-0_sample-X1647


title: DNMT3L_OE_BTS11_3_RNA-seq

data_processing:
adapter and quality trimming using Trim Galore (v0.6.6)
mapped to GRCh38 using Hisat2 (v2.1.0)
Assembly: GRCh38
Supplementary files format and content: Gene expression values are provided for all genes, quantified as RPKM.  Data is provided as a text file.

growth_protocol: Two cell lines of hTSCs (BTS11 and CT29) were obtained from the Arima lab upon written request (Okae et al., 2018). BTS refers to cell lines derived from a blastocyst stage embryo whilst CT originates from 1st trimester placental cytotrophoblast cells.  BTS11 and CT29 were initially cultured using the previously described protocol (Okae et al., 2018) with an updated concentration of CHIR99021 to 4µM (Sheridan et al., 2021). Samples were grown in Okae Media (OM) (Okae et al., 2018). These cells were initially grown in standard 2D conditions until 80% confluent, then technical replicates of each cell line were either maintained in 2D culture conditions. Aliquots of  cells were frozen in PBS at -80°C before proceeding to RNA-sequencing.

extract_protocol:
RNA was extracted pellets of 100,000 cells in 400 μL of TRIzol (Invitrogen) and phase-separated by adding 80 μL of chloroform:isoamyl alcohol (Sigma-Aldrich) after centrifugation at 4 °C for 15 minutes. The aqueous phase was mixed with 1 μL of GlycoBlue and 300 μL of cold isopropanol and incubated on ice for 10 minutes. RNA was pelleted by centrifugation for 10 minutes at 4 °C, washed with 75% ethanol, air-dried, and resuspended in 5 μL of RNase-free water. Oligo (dT)25 capture of mRNA was done using Dynabeads mRNA DIRECT kit (Life Technologies), with previously described adaptations (Hanna et al., 2019).
The SMARTer Stranded RNA-seq kit (Takara) was used to generate libraries from isolated mRNA, using 12 amplification cycles. Libraries were then quantified using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification kit (KAPA).


title: 8wk_HPS1-2_batch-1_sample-X2462


title: 48wk_HPS1-2_batch-0_sample-X1643


title: 16S_H-RF8-T22

description: Library name: Sample 96

data_processing:
For the data processing of rumen microbiomes, raw fastq reads were demultiplexed according to sample-specific barcodes and imported to QIIME2 software (version QIIME2-202402).
The poor-quality bases, adapters and specific primers were trimmed, and the sequences were denoised and binned to amplicon sequence variants (ASVs) using the denoise-paired function of DADA2 plugin for QIIME2.
The feature-classifier plugin was used to construct the specific primer classifiers for the bacteria (341F and 806R of the 16S rRNA gene) based on the SILVA database (version 138). The ASVs were then classified taxonomically based on the specific bacterial classifiers.
The align-to-tree-mafft-fasttree function of the phylogeny plugin was used to construct the phylogenetic trees after the filtering the rare ASVs, and the mitochondria and chloroplast reads. The unweighted unifrac distances for ordination and clustering were calculated using the beta-phylogenetic function of the diversity plugin, and the principal coordinate analysis (PCoA) was performed and visualization by the R software (v4.2) package ggplot2 (v3.4.4).
The alpha diversity parameters (Faith-PD, Chao 1, Shannon, and Simpson) were calculated using the alpha or alpha-phylogenetic function of the diversity plugin. The relative abundance of ruminal bacteria at phylum, family, and genus levels were generated using the relative-frequency function of the feature-table plugin.
Assembly: The V3-V4 region of the prokaryotic small-subunit (16S) rRNA gene was amplified with primers 341F (CCTAYGGGRBGCASCAG) and 806R (GGACTACNNGGGTATCTAAT).
Supplementary files format and content: 16S_feature_table_with_taxonomy.xlsx, 16S-repset-seqs.fasta
Library strategy: 16S rRNA-seq

extract_protocol:
Total genomic DNA was isolated from 1 mL of freeze rumen fluid using TIANamp Stool DNA Kit (DP328, Tiangen) according to manufacturer's instruction.
Amplicon sequencing of rumen 16S rRNA sequencing were performed according to Illumina  protocols with all amplicon libraries being sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA) with 250-base-paired end reads

value: Hay-diet treatment


title: DNMT3L_OE_BTS11_2_RNA-seq


title: 48wk_HPS1-2_batch-0_sample-X1514


title: tFL-P6_cellLine_tazemetostat_RNAseq_repl2

description: B lymphoma cells isolated from a mesenteric lymph node of a R26BCL2+Ezh2Y641F mouse that developed follicular lymphoma were injected into a Rag1KO mouse via IP(passage 1). Lymphoma cells grown in the Rag1KO recipients were isolated and injected into a new Rag1KO mouse (passage 2). We repeated the passages 6 times and finally obtained a lymphoma cells that can proliferate in vitro

data_processing:
RNA sequencing results were aligned to mm10 or T2T-CHM13 using STAR (STAR_2.6.1a) and annotated to RefSeq using the Rsubread package (Rsubread_1.28.1)
Assembly: mm10, hs1T2T_CHM13v2.0
Supplementary files format and content: TPM

source_name: B lymphoma cells

growth_protocol: not applicable

extract_protocol:
Included as additional column of SAMPLES section
RNA was purified with AllPrep DNA/RNA Kit (Qiagen, 80204) and sent to Medgenome for library preparation and sequencing

value: B lymphoma cells

value: Treated with 5 microM tazemetostat for 14 days


title: tFL-P6_cellLine_tazemetostat_RNAseq_repl3


title: DNMT3L_OE_BTS11_1_RNA-seq

value: Trophoblast stem cells


title: BTS11_C1

value: male


title: 16S_H-RF8-T14

description: Library name: Sample 94


title: 18S_G-RF1-T2

description: Library name: Sample 1


title: DNMT3L_OE_BTS11_1

value: 2D culture in okae media in normoxia treated with DNMT3L expressing lentivirus


title: tFL-P6_cellLine_tazemetostat_RNAseq_repl1


title: 48wk_HPS1-2_batch-0_sample-X1434


title: BTS11_C3


title: 16S_H-RF8-T10

description: Library name: Sample 93


title: tFL-P6_cellLine_DMSO_RNAseq_repl3

value: Treated with DMSO for 14 days


title: BTS11_C2_RNA-seq


title: K27_KO3

city: Erlangen

first: Xianyi

last: Meng

address: Glückstr. 6

country: Germany

institute: Department of Medicine 3, Rheumatology and Immunology, University of Erlangen‐Nuremberg

data_processing:
For ChIP-seq the resulting libraries were sequenced on the Illumina HiSeq 2500 platform configured for 50 bp paired-end reads.
ChIP-seq reads were aligned to the mouse (mm9) genomes using Bowtie v2.2.3.
Peaks were called using MACS2 and both bigwig (signal) and bed (peak calls) files were visualized using the integrated genome browser (IGB) genome browser.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: spleen

growth_protocol: Splenic B cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 degree.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a ultrasonicator.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: B cell IgA class switching was induced by LPS (5 μg/ml), BAFF (10 ng/ml), IL-5 (10 ng/ml), TGF-β (10 ng/ml) treatment for 3 days.

value: spleen

value: B cell

value: H3K27ac (ab4734, abcam)


title: tFL-P6_cellLine_DMSO_RNAseq_repl2


title: BTS11_C1_RNA-seq


title: K27_KO2

value: H3K27ac (ab4733, abcam)


title: 16S_H-RF8-T2

description: Library name: Sample 91

value: ruminal fluid


title: K27_KO1

value: H3K27ac (ab4732, abcam)


title: Fexuprazan+HCl_2

city: Seoul

first: Seo Yeon

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

country: South Korea

institute: Yonsei universtiy

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: epithelial cell

value: WT

value: Fexuprazan+HCl


title: 16S_H-RF8-T18

description: Library name: Sample 95


title: Fexuprazan+HCl_1


title: GCB_Ezh2BCL2_RNAseq_repl5

description: DAPI-,B220+Fas+CD38dim at 7 months post bone marrow transplant

source_name: Germinal center B cells

value: Germinal center B cells


title: K27_WT3

value: H3K27ac (ab4731, abcam)


title: GCB_Ezh2BCL2_RNAseq_repl4


title: K27_WT2

value: H3K27ac (ab4730, abcam)


title: BTS11_C3_RNA-seq

value: 2D culture in okae media in normoxia treated with control lentivirus


title: DMSO+HCl_2

value: DMSO+HCl


title: 16S_H-RF7-T14

description: Library name: Sample 88

value: Hay-diet treatment


title: 16S_H-RF7-T10

description: Library name: Sample 87


title: DMSO+HCl_1


title: 16S_H-RF8-T6

description: Library name: Sample 92


title: K27_WT1

value: H3K27ac (ab4729, abcam)


title: K9_KO3

value: H3K9ac (06-947, Upstate)


title: GCB_Ezh2BCL2_RNAseq_repl2


title: GCB_Ezh2BCL2_RNAseq_repl3


title: GCB_Ezh2BCL2_RNAseq_repl1


title: K9_KO2

value: spleen

value: H3K9ac (06-946, Upstate)


title: ThyroidCarcinoma_enzymatic_3

city: Moscow

first: Valentin

last: Trofimov

address: Ulyanova str.11

country: Russia

institute: Endocrinology Research Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1.  (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started)
Assembly: Genome assemblyGRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thyroid carcinoma

extract_protocol:
Single cells were isolated from tissue samples using and enzymatic dissociation method. Approximately 5-250 mg of fresh tissue samples were washed in HBSS, thoroughly minced on ice, and placed in dissociating solution at 37°C with gentle pipetting every 5 minutes.  Tissue samples were dissociated with 25-30 ul enzyme D Multi Tissue Dissociation Kit (MTDK) (Miltenyi Biotec) or enzyme A Neural Tissue Dissociation Kit P (NTDK) (Miltenyi Biotec) or 2 mg/ml collagenase IV (Gibco, Thermo Fisher Scientific) or collagenase I (Gibco, Thermo Fisher Scientific) in 870 mM HBSS, 10% FBS, 20 mM HEPES for 20-30 minutes. Obtained homogenate was filtered in 3-5ml of Wash Buffer (1x DPBS, containing 10% FBS, 20mM HEPES, 6mM glucose) through a pre-wetted 70μm cell culture filter (Miltenyi Biotec) and centrifuged for 5 minutes at 300xg (4 °C).  After all, the pellet was resuspended in a Wash Buffer volume of 100-400 ul, depending on the pellet size.
Single cells were captured and barcoded, and cDNA libraries were generated using the Chromium Next GEM Single Cell 3ʹGEM, Library & Gel Bead Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. Final libraries were multiplexed and sequenced on an Illumina Novaseq 6000 / HiSeq2500 platform, using the S4 Reagent Kit v1.5.

value: thyroid carcinoma

value: enzymatic dissociation


title: 16S_H-RF7-T6

description: Library name: Sample 86

value: ruminal fluid


title: ThyroidCarcinoma_enzymatic_4

description: 10x Genomics


title: tFL-P6_cellLine_DMSO_RNAseq_repl1

value: B lymphoma cells

value: Treated with DMSO for 14 days


title: 16S_H-RF7-T2

description: Library name: Sample 85


title: 16S_H-RF7-T22

description: Library name: Sample 90


title: GCB_BCL2_RNAseq_repl5


title: K9_KO1

value: B cell

value: H3K9ac (06-945, Upstate)


title: 16S_H-RF6-T22

description: Library name: Sample 84


title: GCB_BCL2_RNAseq_repl4

value: Germinal center B cells


title: ThyroidCarcinoma_enzymatic_2

description: 10x Genomics


title: K9_WT3

value: H3K9ac (06-944, Upstate)


title: ThyroidCarcinoma_enzymatic_1

description: 10x Genomics


title: 16S_H-RF6-T18

description: Library name: Sample 83


title: GCB_BCL2_RNAseq_repl3


title: 16S_H-RF7-T18

description: Library name: Sample 89


title: 16S_H-RF6-T14

description: Library name: Sample 82


title: K9_WT2

value: H3K9ac (06-943, Upstate)


title: GCB_BCL2_RNAseq_repl2


title: PitNET_enzymatic_4

description: 10x Genomics

source_name: PitNET

value: PitNET


title: IGAB_KO3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for all samples

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

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: HIF-1a knockout

value: B cell differentiation

value: IgA class switching condition


title: PitNET_enzymatic_5

description: 10x Genomics


title: GCB_BCL2_RNAseq_repl1


title: GCB_WT_RNAseq_repl5


title: IGAB_KO2


title: PitNET_enzymatic_2

description: 10x Genomics


title: 16S_H-RF6-T2

description: Library name: Sample 79

value: Hay-diet treatment


title: 16S_H-RF6-T6

description: Library name: Sample 80


title: 16S_H-RF6-T10

description: Library name: Sample 81


title: IGAB_KO1

value: spleen


title: PitNET_enzymatic_1

description: 10x Genomics


title: PitNET_enzymatic_3

description: 10x Genomics


title: 16S_H-RF5-T22

description: Library name: Sample 78


title: GCB_WT_RNAseq_repl3


title: IGAB_WT3

value: WT


title: 16S_H-RF5-T18

description: Library name: Sample 77


title: MedullaryTumor_enzymatic_5

description: 10x Genomics

source_name: adrenal medullary tumor

value: adrenal medullary tumor


title: IGAB_WT2


title: GCB_WT_RNAseq_repl4


title: GCB_WT_RNAseq_repl2


title: 16S_H-RF5-T14

description: Library name: Sample 76


title: GCB_WT_RNAseq_repl1


title: MedullaryTumor_enzymatic_4

description: 10x Genomics

value: enzymatic dissociation


title: IGAB_WT1


title: 16S_H-RF5-T10

description: Library name: Sample 75

value: ruminal fluid


title: MedullaryTumor_enzymatic_3

description: 10x Genomics


title: Patient sample 168

city: Buffalo

first: Jianxin

last: Wang

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description:
Library name: P_168
Targeted RNA-Seq

data_processing:
Raw read counts received from HTG Molecular Diagnostics, Inc. are first bach effect corrected using combat R package and subsequntly normalized using edgeR Bioconductor package.
Supplementary files format and content: Data matrix with sample ID in rows and log2 normalized expression values in columns in a comma separated text file.

source_name: FFPE

extract_protocol: Patient tissue samples were obtained during standard of care treatment from various clinical timepoints and were sent to HTG Molecular Diagnostics, Inc. for targeted sequencing using their HTG EdgeSeq Oncology Biomarker Panel (OBP) consisting of 2549 cancer-associated genes. Raw data was assembled from five batches of separate HTG runs

value: FFPE


title: K9_WT1

value: H3K9ac (06-942, Upstate)


title: 266_6_control3

city: Omaha

first: Moorthy Palanimuthu

last: Ponnusamy

state: Nebraska

address: 42nd and Emile

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

data_processing:
Illumina sequencing and base calls
Raw Reads: FASTQ format: 1.Quality inspection using FastQC;  2.Aligned to human reference genome (hg19)
1.Hierarchical clustering analysis: Gene Cluster and TreeView
2.Differential expression analysis: DESeq2
3.DAVID functional annotation of up- and down-regulated genes
Supplementary files format and content: Comparision between treated and untreated groups; RPKM values

growth_protocol: 266.6 cells were grown with DMEM HG media supplemented with 10% (v/v) FBS (R&D Systems, USA) and antibiotics (100 units/ml penicillin/100g/ml streptomycin, MilliporeSigma, USA) at standard conditions (5% CO2 and 37°C)

extract_protocol:
RNAeasy kit- RNA extraction.  RNA quality was checked with an Agilent Bioanalyzer (Agilent Technologies, Inc.) and all of the RINs (RNA integrity numbers) were 10.
Library preparation was achieved using the Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: CAF- condition media treated up to 40 days

value: acinar tumor

value: Control


title: 16S_H-RF5-T6

description: Library name: Sample 74


title: Patient sample 167

description:
Library name: P_167
Targeted RNA-Seq


title: 266_6_control2


title: MedullaryTumor_enzymatic_2

description: 10x Genomics


title: 266_6_control1


title: MedullaryTumor_enzymatic_1

description: 10x Genomics


title: Patient sample 166

description:
Library name: P_166
Targeted RNA-Seq


title: Patient sample 165

description:
Library name: P_165
Targeted RNA-Seq


title: 266_6_CAF_CM_treated3

value: CAF-CM treated


title: AdrenocorticalTumor_enzymatic_3

description: 10x Genomics

source_name: adrenocortical tumor

value: adrenocortical tumor


title: AdrenocorticalTumor_enzymatic_2

description: 10x Genomics


title: Patient sample 164

description:
Library name: P_164
Targeted RNA-Seq


title: 266_6_CAF_CM_treated2


title: 16S_H-RF4-T18

description: Library name: Sample 71


title: Patient sample 163

description:
Library name: P_163
Targeted RNA-Seq


title: 16S_H-RF4-T14

description: Library name: Sample 70


title: 266_6_CAF_CM_treated1


title: AdrenocorticalTumor_enzymatic_1

description: 10x Genomics


title: ThyroidCarcinoma_ACME_1

description: 10x Genomics

extract_protocol:
Single cells were isolated from tissue samples using ACME HS followed by cryopreservation in 3xSSC*10% DMSO and methanol cell fixation. Key adaptations of the ACME HS method were the supplement of solution composition with 0.1M NAC and the introduction of additional washing steps in cold high salt 3xSSC* buffer. ACME dissociation was conducted in ~ 1 hours on a rotator at room temperature, with periodic pipetting of the solution. Afterward, we removed the ACME solution and washed the pellet with a two-step washing in cold 3xSSC.
Single cells or nuclei were captured and barcoded, and cDNA libraries were generated using the Chromium Next GEM Single Cell 3ʹGEM, Library & Gel Bead Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. Final libraries were multiplexed and sequenced on an Illumina Novaseq 6000 platform, using the S4 Reagent Kit v1.5 and Illumina HiSeq2500 platform.

value: thyroid carcinoma

value: ACME HS dissociation


title: Patient sample 162

description:
Library name: P_162
Targeted RNA-Seq


title: tracheal epithelial cells, 3 inhibitors (Y-27632+A8301+DMH-1), rep3

city: Shanghai

first: Yalin

last: He

address: No. 320, Yueyang Road, Xuhui District

institute: Center for Excellence in Molecular Cell Science

data_processing:
The sequencing reads were aligned to the GRCm39 using Hisat2 (v2.1.0).
Rsubread (v2.10.5) R package was used to obtain gene counts from BAM files.
Count normalization was performed by DESeq2 (v1.36.0) R package.
Assembly: GRCm39
Supplementary files format and content: csv file include DESeq2 normalized count

source_name: trachea

extract_protocol:
1-1.5 μg of total RNA were used for preparing RNA-seq libraries.
RNA-seq libraries were prepared using VAHTS universal V8 RNA-seq Library Prep kit for Illumina (Vazyme, NR605) according to the manufacturer’s instructions.

value: trachea

value: primary mouse airway basal stem cells

value: epithelial cells


title: PitNET_ACME_2

description: 10x Genomics

value: PitNET


title: Patient sample 161

description:
Library name: P_161
Targeted RNA-Seq


title: tracheal epithelial cells, 3 inhibitors (Y-27632+A8301+DMH-1), rep2


title: 16S_H-RF5-T2

description: Library name: Sample 73

value: Hay-diet treatment


title: Patient sample 160

description:
Library name: P_160
Targeted RNA-Seq


title: PitNET_ACME_1

description: 10x Genomics


title: tracheal epithelial cells, 3 inhibitors (Y-27632+A8301+DMH-1), rep1

value: WT


title: 16S_H-RF4-T22

description: Library name: Sample 72


title: 16S_H-RF3-T22

description: Library name: Sample 66


title: 16S_H-RF3-T18

description: Library name: Sample 65


title: tracheal epithelial cells, UK-5099, rep2


title: Patient sample 158

description:
Library name: P_158
Targeted RNA-Seq


title: MedullaryTumor_ACME_4

description: 10x Genomics

value: adrenal medullary tumor


title: tracheal epithelial cells, UK-5099, rep1


title: MedullaryTumor_ACME_3

description: 10x Genomics


title: Patient sample 157

description:
Library name: P_157
Targeted RNA-Seq


title: 16S_H-RF3-T10

description: Library name: Sample 63


title: MedullaryTumor_ACME_2

description: 10x Genomics


title: 16S_H-RF4-T10

description: Library name: Sample 69


title: 16S_H-RF3-T6

description: Library name: Sample 62


title: Patient sample 156

description:
Library name: P_156
Targeted RNA-Seq


title: 16S_H-RF3-T14

description: Library name: Sample 64


title: Patient sample 155

description:
Library name: P_155
Targeted RNA-Seq


title: tracheal epithelial cells rep2, ALI culture, D5

value: Epithelial cells

tag: time point

value: ALI culture


title: MedullaryTumor_ACME_1

description: 10x Genomics


title: 16S_H-RF4-T6

description: Library name: Sample 68

value: ruminal fluid


title: Patient sample 159

description:
Library name: P_159
Targeted RNA-Seq

value: FFPE


title: AdrenocorticalTumor_ACME_5

description: 10x Genomics


title: 16S_H-RF3-T2

description: Library name: Sample 61


title: 16S_H-RF4-T2

description: Library name: Sample 67


title: MedullaryTumor_ACME_5

description: 10x Genomics


title: tracheal epithelial cells rep1, ALI culture, D5


title: AdrenocorticalTumor_ACME_4

description: 10x Genomics


title: Patient sample 154

description:
Library name: P_154
Targeted RNA-Seq


title: Patient sample 153

description:
Library name: P_153
Targeted RNA-Seq


title: tracheal epithelial cells, UK-5099, rep3


title: tracheal epithelial cells rep3, ALI culture, D3


title: 16S_H-RF2-T18

description: Library name: Sample 59


title: AdrenocorticalTumor_ACME_3

description: 10x Genomics


title: tracheal epithelial cells rep2, ALI culture, D3


title: Patient sample 152

description:
Library name: P_152
Targeted RNA-Seq


title: tracheal epithelial cells rep3, ALI culture, D5


title: tracheal epithelial cells rep1, ALI culture, D3


title: AdrenocorticalTumor_ACME_2

description: 10x Genomics


title: Patient sample 149

description:
Library name: P_149
Targeted RNA-Seq


title: Patient sample 150

description:
Library name: P_150
Targeted RNA-Seq


title: Patient sample 151

description:
Library name: P_151
Targeted RNA-Seq


title: tracheal epithelial cells rep2, ALI culture, D1


title: ARID1A-knockout 293T, O/E ARID1A ΔIDR1b, O/E EWS-FLI1, repeat 1

first: Bing

address: South Chongqing Road 280

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format
Fastp (version 0.23.1) was used to perform basic statistics on the quality of the raw reads
The reads in the sequencing results were aligned with the reference genome GRCh38 (hg38) using STAR, the mapped reads were screened by samtools rmdup tool to exclude PCR duplicates, and the gene expression of each group data was calculated using featureCount tool.
The obtained gene expression results were analyzed by edgeR package in R studio software, and the significantly differentially expressed genes (Fold Change greater than 2 or less than 0.5, p value less than 0.05)
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: HEK-293T cells were maintained in DMEM supplemetary with 10% fetal bovine serum (FBS) and antibiotics in humidified atmospherein with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with Trizol reagent, polyA RNA was enriched with Oligo(dT) magnetic beads
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified.

treatment_protocol: The cells was transfected with 2ug pcDNA-EWS-FLI1 plasmid and continue to growth for 48h

value: Human Embryonic Kidney

value: ARID1A knockout, O/E ARID1A delta-IDR1b

value: O/E EWS-FLI1


title: ARID1A-knockout 293T, O/E ARID1A ΔIDR1b, O/E EWS-FLI1, repeat 2


title: 16S_H-RF2-T10

description: Library name: Sample 57


title: tracheal epithelial cells rep3, ALI culture, D1


title: 16S_H-RF2-T22

description: Library name: Sample 60


title: Patient sample 147

description:
Library name: P_147
Targeted RNA-Seq


title: airway basal stem cells, acetate treated Mpc2-deficient basal cells, H3 pan-ac, rep3

data_processing:
The CUT&Tag reads were aligned to the mm10 reference genome with Bowtie2 (v2.3.4.2).
PCR duplicated reads were removed with Picard.
The resulting deduplicated BAM files were normalized to the total aligned reads with the bamCoverage command from deepTools (v3.5.1).
The normalized signals of CUT&Tag were converted into Bigwig using bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
105 ALI-cultured basal cells were collected and bound to ConA beads for 10 minutes at room temperature. This was followed by an overnight incubation with the Histone H3ac (pan-acetyl) antibody at 4°C. After the secondary antibody incubation, the cells were mixed with 0.04 μM pA/G–Tnp for 1 hour at room temperature, and then subjected to tagmentation and DNA extraction.
The libraries were constructed using the 'TD903 Hyperactive Universal CUT&Tag Assay Kit for Illumina' and the 'TD202 TruePrep Index Kit V2 for Illumina' (Vazyme).

value: epithelial cell

value: p63CreER; Mpc2f/f

value: acetate


title: Patient sample 148

description:
Library name: P_148
Targeted RNA-Seq


title: tracheal epithelial cells rep1, ALI culture, D1

value: trachea


title: ARID1A-knockout 293T, O/E ARID1A ΔIDR1b, O/E empty vector, repeat 2

value: O/E empty vector


title: 16S_H-RF1-T18

description: Library name: Sample 53


title: Patient sample 146

description:
Library name: P_146
Targeted RNA-Seq


title: ARID1A-knockout 293T, O/E ARID1A WT, O/E EWS-FLI1, repeat 2

value: ARID1A knockout, O/E ARID1A WT


title: 16S_H-RF2-T14

description: Library name: Sample 58


title: Patient sample 145

description:
Library name: P_145
Targeted RNA-Seq


title: 16S_H-RF1-T14

description: Library name: Sample 52


title: AdrenocorticalTumor_ACME_1

description: 10x Genomics

value: adrenocortical tumor

value: ACME HS dissociation


title: ARID1A-knockout 293T, O/E ARID1A WT, O/E EWS-FLI1, repeat 1


title: 16S_H-RF1-T10

description: Library name: Sample 51

value: Hay-diet treatment


title: airway basal stem cells, Mpc2-deficient basal cells, H3 pan-ac, rep3

value: primary mouse airway basal stem cells


title: 16S_H-RF2-T6

description: Library name: Sample 56


title: Patient sample 144

description:
Library name: P_144
Targeted RNA-Seq


title: 16S_H-RF2-T2

description: Library name: Sample 55


title: Patient sample 143

description:
Library name: P_143
Targeted RNA-Seq


title: 16S_H-RF1-T6

description: Library name: Sample 50


title: 16S_H-RF1-T22

description: Library name: Sample 54


title: 16S_H-RF1-T2

description: Library name: Sample 49


title: ARID1A-knockout 293T, O/E ARID1A WT, O/E empty vector, repeat 2


title: ARID1A-knockout 293T, O/E ARID1A WT, O/E empty vector, repeat 1


title: Patient sample 142

description:
Library name: P_142
Targeted RNA-Seq


title: airway basal stem cells, acetate treated Mpc2-deficient basal cells, H3 pan-ac, rep2


title: ARID1A-knockout 293T, O/E ARID1A ΔIDR1b, O/E empty vector, repeat 1


title: ARID1A-knockout 293T, O/E empty vector, O/E EWS-FLI1, repeat 2

value: ARID1A knockout


title: 16S_G-RF8-T22

description: Library name: Sample 48

value: Grain-diet treatment


title: ARID1A-knockout 293T, O/E empty vector, O/E EWS-FLI1, repeat 1


title: 16S_G-RF8-T18

description: Library name: Sample 47

value: ruminal fluid


title: airway basal stem cells, acetate treated Mpc2-deficient basal cells, H3 pan-ac, rep1


title: airway basal stem cells, WT, H3 pan-ac, rep3

value: WT


title: airway basal stem cells, WT, H3 pan-ac, rep2


title: Patient sample 140

description:
Library name: P_140
Targeted RNA-Seq

value: FFPE


title: ARID1A-knockout 293T, O/E empty vector, O/E empty vector, repeat 2

value: Human Embryonic Kidney


title: Patient sample 139

description:
Library name: P_139
Targeted RNA-Seq


title: airway basal stem cells, WT, H3 pan-ac, rep1


title: 16S_G-RF8-T14

description: Library name: Sample 46


title: ARID1A-knockout 293T, O/E empty vector, O/E empty vector, repeat 1


title: 16S_G-RF8-T10

description: Library name: Sample 45


title: Patient sample 138

description:
Library name: P_138
Targeted RNA-Seq


title: Mutant ATAC Sample 3

city: San Antonio

first: Luke

last: Norton

state: Texas

address: 7703 Floyd Curl Dr

institute: UTHSCSA

data_processing:
Gene counting, peak calling, barcode processing, and aggregation were done using the Cell Ranger Arc v2.0.2 software (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Liver

extract_protocol:
Nuclei were isolated from approximately 20 mg of frozen mouse liver harvested from control (TCF7L2LoxP/LoxP) and liver-specific TCF7L2 mutant mice (Hep-TCF7L2ΔDBD). 10X Genomics Chromium single nuclei multiome gene expression and Assay for Transposase-Accessible Chromatin (ATAC) libraries were prepared from approximately 5000 nuclei/mice at the Genome Sequencing Facility at the University of Texas Health at San Antonio (UTHSA). Liver samples were processed in pairs (one control and one mutant) on three consecutive days to minimize batch effects. Library quality and quantity were assessed using the 2100 Bioanalyzer and were sequenced on a NovaSeq 6000 (Illumina, CA, USA).
Starting with frozen tissue, a wide range of sample types can be dissociated with the Chromium Nuclei Isolation Kit. The resulting single nuclei suspension is transposed in bulk before partitioning into GEMs on the Chromium instrument. DNA fragments and the 3’ ends of mRNA from individual nuclei are identified with unique 10x Barcodes. Two complementary libraries are generated from each sample, followed by sequencing and data analysis. 10x Barcodes are used to associate reads back to cells of origin, and gene expression and open chromatin profiles are linked with certainty
10X Single Cell Multiome ATAC + Gene Expression

value: Liver


title: airway basal stem cells, Mpc2-deficient basal cells, H3 pan-ac, rep2

value: epithelial cell


title: 16S_G-RF8-T6

description: Library name: Sample 44

source_name: ruminal fluid


title: Patient sample 137

description:
Library name: P_137
Targeted RNA-Seq


title: Patient sample 136

description:
Library name: P_136
Targeted RNA-Seq


title: Patient sample 141

description:
Library name: P_141
Targeted RNA-Seq


title: PitNET_nuclei_2

description: 10x Genomics

extract_protocol:
Nuclei were isolated from fresh-frozen adrenocortical tumor, adrenal medullary tumor, and PitNET specimens. Fresh-frozen tissue samples were thoroughly minced on ice and placed into a gentleMACS C tube (Miltenyi Biotec) with 2ml ice-cold Hypotonic lysis buffer (10mM HEPES pH7.2, 5mM MgCl2, 10mM NaCl, 1% NP40). GentleMACS C tubes were then placed on the gentleMACS Dissociator (Miltenyi Biotec) and samples were homogenized by running the program h_mito_01, and then incubated on ice for 10 minutes. After repeating the homogenization step, 2 ml of Isotonic buffer (10mM HEPES pH7.2, 5mM MgCl2,10mM NaCl, 500mM sucrose) was added to the lysates, mixed by pipetting, filtered through a pre-wetted 70μm cell culture filter (Miltenyi Biotec) with Isotonic wash buffer (10mM HEPES pH7.2, 5mM MgCl2,10mM NaCl, 250mM sucrose) and centrifuged for 5 minutes at 1000g (4 °C). Then, we carefully removed the supernatant, resuspended the pellet in 1 ml DPBS with 1% BSA, and filtered it through a pre-wetted 30μm cell culture filter (Miltenyi Biotec). After all, the pellet was resuspended in DPBS containing 1% BSA volume 100-400 ul, depending on the pellet size.
Nuclei were captured and barcoded, and cDNA libraries were generated using the Chromium Next GEM Single Cell 3ʹGEM, Library & Gel Bead Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. Final libraries were multiplexed and sequenced on an Illumina Novaseq 6000 platform.

value: PitNET

value: nuclei extraction


title: PitNET_nuclei_1

description: 10x Genomics


title: 16S_G-RF8-T2

description: Library name: Sample 43


title: Control ATAC Sample 3


title: Mutant ATAC Sample 2


title: MedullaryTumor_nuclei_5

description: 10x Genomics

value: adrenal medullary tumor


title: Mutant ATAC Sample 1


title: Patient sample 135

description:
Library name: P_135
Targeted RNA-Seq


title: MedullaryTumor_nuclei_4

description: 10x Genomics


title: 16S_G-RF7-T18

description: Library name: Sample 41


title: MedullaryTumor_nuclei_3

description: 10x Genomics


title: Patient sample 133

description:
Library name: P_133
Targeted RNA-Seq


title: Patient sample 134

description:
Library name: P_134
Targeted RNA-Seq


title: Control ATAC Sample 2


title: Control ATAC Sample 1


title: Patient sample 132

description:
Library name: P_132
Targeted RNA-Seq


title: 16S_G-RF7-T14

description: Library name: Sample 40


title: Mutant GEX Sample 3

molecule: nuclear RNA


title: MedullaryTumor_nuclei_2

description: 10x Genomics


title: 16S_G-RF7-T10

description: Library name: Sample 39


title: Mutant GEX Sample 2


title: 16S_G-RF7-T6

description: Library name: Sample 38


title: Patient sample 131

description:
Library name: P_131
Targeted RNA-Seq


title: AdrenocorticalTumor_nuclei_2

description: 10x Genomics


title: 16S_G-RF7-T22

description: Library name: Sample 42


title: Mutant GEX Sample 1


title: Patient sample 129

description:
Library name: P_129
Targeted RNA-Seq


title: Patient sample 130

description:
Library name: P_130
Targeted RNA-Seq


title: 16S_G-RF6-T22

description: Library name: Sample 36


title: Control GEX Sample 3


title: AdrenocorticalTumor_nuclei_1

description: 10x Genomics


title: 16S_G-RF6-T18

description: Library name: Sample 35


title: PDX_DLBCL-EZB_tazemetostat_RNAseq_repl5

description: EZH2-mutant DLBCL PDX were grown in NSG mice and treated with either tazemetostat or vehicle for 14 days in vivo. Tumor tissues were isolated from mice at the end of the treatment and put into RNAlater (Thermo) for RNA extraction.

source_name: Patient derived xenograft

value: Patient derived xenograft

value: t(14;18) translocation; EZH2Y641F

value: 250 mg/kg tazemetostat PO, BID for 14 days


title: Patient sample 128

description:
Library name: P_128
Targeted RNA-Seq


title: PDX_DLBCL-EZB_tazemetostat_RNAseq_repl4


title: Control GEX Sample 1


title: Patient sample 127

description:
Library name: P_127
Targeted RNA-Seq


title: 16S_G-RF6-T14

description: Library name: Sample 34


title: PDX_DLBCL-EZB_tazemetostat_RNAseq_repl3


title: 16S_G-RF6-T10

description: Library name: Sample 33


title: Patient sample 126

description:
Library name: P_126
Targeted RNA-Seq


title: 16S_G-RF6-T6

description: Library name: Sample 32


title: MedullaryTumor_nuclei_1

description: 10x Genomics


title: PDX_DLBCL-EZB_tazemetostat_RNAseq_repl2


title: Monocyte_RNA_Plas_CLP rep2

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 150-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Assembly: mm39
Supplementary files format and content: .gene.mmseq files contain counts per gene

source_name: bone marrow

growth_protocol: Mice were infected with Plasmodium yoelii for 6 weeks and then infected with CLP or left untreated for additional 3 hours. Mice were then sacrificed and bone marrow were harvested for HSPC, GMP or monoctes isolation.

extract_protocol:
Different cells were sorted by BD Aria III with the following surface markers. HSPCs were sorted from Lin- cKit+ CD34+ population. GMPs were sorted from Lin-Ckit+Sca1-Cd16/32+CD34- population. Monocytes were sorted from CD45+CD11b+Ly6Chi Ly6G- population.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

treatment_protocol: Monocytes collected from mice 6 weeks after Py infection and following CLP

value: monocyte


title: PDX_DLBCL-EZB_tazemetostat_RNAseq_repl1


title: Patient sample 125

description:
Library name: P_125
Targeted RNA-Seq


title: Monocyte_RNA_Plas_CLP rep1


title: 16S_G-RF6-T2

description: Library name: Sample 31


title: 16S_G-RF7-T2

description: Library name: Sample 37


title: Patient sample 124

description:
Library name: P_124
Targeted RNA-Seq


title: Monocyte_RNA_PBS_CLP rep2

treatment_protocol: Naive monocytes, from mice treated with PBS and following CLP


title: PDX_DLBCL-EZB_vehicle_RNAseq_repl5

value: Vehicle PO, BID for 14 days


title: Control GEX Sample 2


title: Patient sample 123

description:
Library name: P_123
Targeted RNA-Seq


title: Monocyte_RNA_PBS_CLP rep1


title: Patient sample 122

description:
Library name: P_122
Targeted RNA-Seq


title: 16S_G-RF5-T14

description: Library name: Sample 28


title: 16S_G-RF5-T18

description: Library name: Sample 29


title: PDX_DLBCL-EZB_vehicle_RNAseq_repl4


title: PDX_DLBCL-EZB_vehicle_RNAseq_repl3


title: Monocyte_RNA_Plas rep1

treatment_protocol: Monocytes collected from mice 6 weeks after Py infection


title: Patient sample 121

description:
Library name: P_121
Targeted RNA-Seq


title: PDX_DLBCL-EZB_vehicle_RNAseq_repl2


title: 16S_G-RF5-T10

description: Library name: Sample 27


title: Patient sample 120

description:
Library name: P_120
Targeted RNA-Seq


title: Monocyte_RNA_PBS rep2

treatment_protocol: Naive monocytes, from mice treated with PBS


title: PDX_DLBCL-EZB_vehicle_RNAseq_repl1


title: Patient sample 119

description:
Library name: P_119
Targeted RNA-Seq


title: Monocyte_RNA_PBS rep1


title: PE7

city: Shenyang

first: XUAN

last: ZHANG

state: Liaoning

address: Shenyang 110004, People's Republic of China.

institute: Shengjing Hospital of China Medical University

data_processing:
Real-Time Analysis (version 3.4.4) and bcl2fastq (version 2.19 ).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.1).
Trimmed sequence reads were mapped to GRCh38/hg38 using hisat2 with default parameters.
Read count extraction were performed using htseq-count,and normalized counts using FPKM (Fragments Per Kilobase Million).
Assembly: hg38
Supplementary files format and content: processed data.xlsx

source_name: placenta

extract_protocol:
Total RNAs were isolated from placental samples with Trizol (Invitrogen, California, USA).   Samples (≥ 1 μg) of RNA integrity number (RIN)  ≥  7.0 and OD260/280  ≥  1.8 were subjected to RNA-seq.
RNA libraries for RNA-seq were prepared using  Invitrogen SuperScript™ II Reverse Transcriptase following the manufacturer's protocols.

value: placenta


title: Patient sample 118

description:
Library name: P_118
Targeted RNA-Seq


title: GMP_RNA_Plas rep2

treatment_protocol: GMPs collected from mice 6 weeks after Py infection

value: granulocyte-macrophage progenitors


title: 16S_G-RF4-T22

description: Library name: Sample 24

value: Grain-diet treatment


title: 16S_G-RF5-T2

description: Library name: Sample 25

value: ruminal fluid


title: GMP_RNA_Plas rep1


title: Patient sample 117

description:
Library name: P_117
Targeted RNA-Seq


title: 16S_G-RF5-T22

description: Library name: Sample 30


title: 16S_G-RF4-T18

description: Library name: Sample 23


title: PE4


title: Monocyte_RNA_Plas rep2


title: Patient sample 116

description:
Library name: P_116
Targeted RNA-Seq


title: PE3


title: 16S_G-RF4-T14

description: Library name: Sample 22


title: PE2


title: GMP_RNA_PBS rep1

treatment_protocol: Naive GMPs, from mice treated with PBS


title: Patient sample 115

description:
Library name: P_115
Targeted RNA-Seq


title: GMP_RNA_PBS rep2


title: NP9


title: Patient sample 114

description:
Library name: P_114
Targeted RNA-Seq


title: HSPC_RNA_Plas

treatment_protocol: HSPCs collected from mice 6 weeks after Py infection

value: hematopoietic stem and progenitor cells


title: NP8


title: Patient sample 113

description:
Library name: P_113
Targeted RNA-Seq

value: FFPE


title: 16S_G-RF5-T6

description: Library name: Sample 26


title: HSPC_RNA_PBS

treatment_protocol: Naive HSPCs, from mice treated with PBS


title: 16S_G-RF4-T10

description: Library name: Sample 21


title: NP7


title: Patient sample 112

description:
Library name: P_112
Targeted RNA-Seq


title: NP6


title: 16S_G-RF3-T22

description: Library name: Sample 18


title: 16S_G-RF4-T2

description: Library name: Sample 19


title: Monocyte_Plas_1

data_processing:
ATAC-seq reads were aligned to the mm39 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for ATAC signal at p-value of 10-5 using the default (narrow) setting.
Assembly: mm39
Supplementary files format and content: BigWig files for visualization

extract_protocol:
Different cells were sorted by BD Aria III with the following surface markers. HSPCs were sorted from Lin- cKit+ CD34+ population. GMPs were sorted from Lin-Ckit+Sca1-Cd16/32+CD34- population. Monocytes were sorted from CD45+CD11b+Ly6Chi Ly6G- population.
Library preparation was performed using the Ovation Ultralow DNA-seq library preparation kit and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 30 million reads per sample.


title: Patient sample 110

description:
Library name: P_110
Targeted RNA-Seq


title: NP4


title: NP5


title: 16S_G-RF3-T14

description: Library name: Sample 16

extract_protocol:
Total genomic DNA was isolated from 1 mL of freeze rumen fluid using TIANamp Stool DNA Kit (DP328, Tiangen) according to manufacturer's instruction.
Amplicon sequencing of rumen 16S rRNA sequencing were performed according to Illumina  protocols with all amplicon libraries being sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA) with 250-base-paired end reads


title: Patient sample 109

description:
Library name: P_109
Targeted RNA-Seq


title: Monocyte_PBS_1


title: 16S_G-RF3-T18

description: Library name: Sample 17


title: Monocyte_PBS_2


title: 16S_G-RF3-T10

description: Library name: Sample 15


title: GMP_Plas_2


title: Patient sample 108

description:
Library name: P_108
Targeted RNA-Seq


title: Patient sample 111

description:
Library name: P_111
Targeted RNA-Seq


title: N3_sequence

city: Jinan

first: Xiumei

state: Shandong

address: Wenhua Xi Road

institute: Department of Clinical Laboratory, Qilu Hospital, Shandong University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4).
HTSeq software (v0.9.1) was used to get the raw count.
edgeR was used to perform normalization.
Differentially expressed lncRNAs were identified by p-value and fold change.
Assembly: h19
Supplementary files format and content: excel format   gene expression profiling
Supplementary files format and content: FPKM counts

source_name: serum

extract_protocol:
RNA was extracted using trizol LS reagent.
Total RNA was used for removing the rRNAs.The rRNA-depleted samples were subjected to library construction with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

value: serum

value: non-muscle-invasive bladder cancer


title: N4_sequence


title: 16S_G-RF4-T6

first: Yongkang

address: Yangzhou University

institute: Yangzhou University

description: Library name: Sample 20


title: Patient sample 107

description:
Library name: P_107
Targeted RNA-Seq


title: GMP_Plas_1


title: Patient sample 106

description:
Library name: P_106
Targeted RNA-Seq


title: Monocyte_Plas_2


title: 16S_G-RF3-T2

description: Library name: Sample 13


title: GMP_PBS_2


title: N2_sequence


title: 16S_G-RF3-T6

description: Library name: Sample 14


title: N1_sequence


title: 16S_G-RF2-T22

description: Library name: Sample 12


title: Patient sample 105

description:
Library name: P_105
Targeted RNA-Seq


title: M4_sequence

value: muscle-invasive bladder cancer


title: Patient sample 104

description:
Library name: P_104
Targeted RNA-Seq


title: HSPC_Plas_2


title: M3_sequence


title: Patient sample 102

description:
Library name: P_102
Targeted RNA-Seq


title: HSPC_Plas_1


title: Patient sample 103

description:
Library name: P_103
Targeted RNA-Seq


title: 16S_G-RF2-T10

description: Library name: Sample 9


title: M2_sequence


title: HSPC_PBS_2


title: M1_sequence


title: 16S_G-RF2-T6

description: Library name: Sample 8


title: HSPC_PBS_1


title: CPL 3

first: Liu

middle: Ming

last: Jie

address: 44 wenhua west road

institute: Shandong University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)   by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2(v2.0.4) .
Bowtie2 (v2.2.5)   was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Differential expression was performed using DESeq2 (version 1.4.5).
Assembly: Homo_sapiens.GRCh38.dna.toplevel.REF.fa
Supplementary files format and content: Text Document  include Raw read counts for each Sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1ug of total RNA for the construction.RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSEQ  platform.

value: CPL


title: Patient sample 101

description:
Library name: P_101
Targeted RNA-Seq


title: 16S_G-RF2-T2

description: Library name: Sample 7

data_processing:
For the data processing of rumen microbiomes, raw fastq reads were demultiplexed according to sample-specific barcodes and imported to QIIME2 software (version QIIME2-202402).
The poor-quality bases, adapters and specific primers were trimmed, and the sequences were denoised and binned to amplicon sequence variants (ASVs) using the denoise-paired function of DADA2 plugin for QIIME2.
The feature-classifier plugin was used to construct the specific primer classifiers for the bacteria (341F and 806R of the 16S rRNA gene) based on the SILVA database (version 138). The ASVs were then classified taxonomically based on the specific bacterial classifiers.
The align-to-tree-mafft-fasttree function of the phylogeny plugin was used to construct the phylogenetic trees after the filtering the rare ASVs, and the mitochondria and chloroplast reads. The unweighted unifrac distances for ordination and clustering were calculated using the beta-phylogenetic function of the diversity plugin, and the principal coordinate analysis (PCoA) was performed and visualization by the R software (v4.2) package ggplot2 (v3.4.4).
The alpha diversity parameters (Faith-PD, Chao 1, Shannon, and Simpson) were calculated using the alpha or alpha-phylogenetic function of the diversity plugin. The relative abundance of ruminal bacteria at phylum, family, and genus levels were generated using the relative-frequency function of the feature-table plugin.
Assembly: The V3-V4 region of the prokaryotic small-subunit (16S) rRNA gene was amplified with primers 341F (CCTAYGGGRBGCASCAG) and 806R (GGACTACNNGGGTATCTAAT).
Supplementary files format and content: 16S_feature_table_with_taxonomy.xlsx, 16S-repset-seqs.fasta
Library strategy: 16S rRNA-seq


title: Patient sample 100

description:
Library name: P_100
Targeted RNA-Seq


title: Patient sample 99

description:
Library name: P_99
Targeted RNA-Seq


title: CPL 2


title: CPL 1


title: S.6759

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

institute: University of Arkansas for Medical Sciences

data_processing:
Fastq quality check: FastQC,v0.11.8
Fastq trimming: Trimmomatic, v0.39
Alignment: Hisat2,version 2.2.1
Assembly: Mus musculus GRCm39.104
Supplementary files format and content: counts

source_name: FFPE - mouse liver cancer

growth_protocol: To evaluate the in vivo therapeutic efficacy of the MMR vaccine in subcutaneous mouse HCC model, 1  106 Hepa 1-6 in 100 µL of cold RPMI were injected subcutaneously into the right flanks of immunocompetent female C57L mice (n=7/group [Hepa 1-6] Jackson Laboratories) using 1 mL syringes. Mice were monitored weekly for palpable tumors or any changes in appearance or behavior. When average tumors reached a treatable size (80-120 mm3), mice were randomized into the respective study groups and dosed within 24 hours of randomization.

extract_protocol:
Hepa 1-6 FFPE scrolls were processed for DNA and RNA extraction using a Quick-DNA/RNA FFPE Miniprep Kit with on-column DNase digestion for the RNA preps (Cat. # R1009; Zymo Research). RNA was assessed for mass concentration using the Qubit RNA Broad Range Assay Kit (Cat. # Q10211; Invitrogen) with a Qubit 4 fluorometer (Cat. # Q33238; Invitrogen). RNA quality was assessed with a Standard Sensitivity RNA Analysis Kit (Cat. # DNF-471-0500; Agilent) on a Fragment Analyzer System (Cat. # M5310AA; Agilent).
Sequencing libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold (Cat. # 20020599; Illumina). RNA DV200 scores were used to determine fragmentation times. Libraries were assessed for mass concentration using a Qubit 1X dsDNA HS Assay Kit (Cat. # Q33231; Invitrogen) with a Qubit 4 fluorometer (Cat. # Q33238; Invitrogen). Library fragment size was assessed with a High Sensitivity NGS Fragment Analysis Kit (Cat. # DNF-474-0500; Agilent) on a Fragment Analyzer System (Cat. # M5310AA; Agilent). Libraries were functionally validated with a KAPA Universal Library Quantification Kit (Cat. # 07960140001; Roche). Sequencing was performed to generate paired-end reads (2  100 bp) with a 200-cycle S1 flow cell on a NovaSeq 6000 sequencing system (Illumina).

treatment_protocol: On days 0, 7, and 14, mice were administered 50 µL IT injections containing PBS (PBS control groups) or 1  102 TCID50 units (a 10-fold lower dose compared to the immunizing dose used in children) of MMR (MMR groups). Tumor volume and body weight were measured twice weekly following randomization and initiation of treatment using a digital caliper and balance. Tumor volume was calculated using the following equation: (longest diameter * shortest diameter2)/2 with a digital caliper. During the first week of treatment and after each injection, mice were monitored daily for signs of recovery for up to 72 hours. Mice were euthanized when body weight loss exceeded 20%, when tumor size was larger than 2,000 m³, or for adverse effects of treatment. Mice were sacrificed 28 (Hepa 1-6 cohort) days following the first MMR dose administration, at which time tumor and blood were collected for downstream analysis.

value: liver cancer

tag: injected cell line

tag: condition

value: MMR (3 times , once week)


title: S.3896


title: Patient sample 98

description:
Library name: P_98
Targeted RNA-Seq


title: 16S_G-RF1-T22

city: Yangzhou

last: Zhen

description: Library name: Sample 6


title: 16S_G-RF1-T18

description: Library name: Sample 5


title: GMP_PBS_1


title: Ctrl 3

value: Placebo


title: airway basal stem cells, Mpc2-deficient basal cells, H3 pan-ac, rep1

value: trachea

value: primary mouse airway basal stem cells

value: epithelial cell

value: p63CreER; Mpc2f/f


title: 16S_G-RF2-T18

description: Library name: Sample 11


title: 16S_G-RF1-T14

description: Library name: Sample 4


title: 16S_G-RF2-T14

description: Library name: Sample 10


title: Patient sample 97

description:
Library name: P_97
Targeted RNA-Seq


title: S.6707-L

value: (4-74970) Dual flanks


title: Patient sample 96

description:
Library name: P_96
Targeted RNA-Seq


title: Ctrl 2


title: 16S_G-RF1-T6

description: Library name: Sample 2


title: S.6707


title: Ctrl 1


title: Patient sample 95

description:
Library name: P_95
Targeted RNA-Seq


title: S.6704-X

value: (31-74970) Dual flanks


title: S.6760


title: ChIP-seq SPT5-pCTR1_PSIP1ΔIBD

city: nanjing

first: shuhan

last: si

state: jiangsu

address: sipailou

institute: Southeast University

data_processing:
Adaptors and low-quality reads removal were performed using Trim Galore v0.6.7 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the parameter ‘‘-q 20’’
Paired-reads were aligned to mouse human hg19 using Bowtie v2.4.5 with default parameters
Normalized bigwig and Log2 fold change of ChIP-seq signal were generated using deepTools v 3.5.1 bamCoverage and bigwigCompare
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: The HCT 116 cell lines were cultured in DMEM (HyClone) supplemented with 10% FBS (Ex-Cell Bio), 1% Penicillin-Streptomycin (HyClone), and maintained at 37°C incubators with 5% CO2. For passaging, cells were washed with 1 × PBS (Hyclone). 0.25% Trypsin-EDTA (Gibco) was used to detach cells from plates. Trypsin-EDTA was quenched by addition of FBS containing media. For serum stimulation, cells were first starved by washing three times with 1 × PBS and culturing for 40 hours in serum free media, then either left untreated or treated with serum for indicated time before harvesting.

extract_protocol:
ChIP was performed as previously described. First, approximately 2× 107 HCT 116 cells were crosslinked using 1% formaldehyde (Sigma) at room temperature for 10 minutes, and cross-linking was quenched by glycine (final concentration is 125 mM) for 5 minutes. Then, cells were rinsed twice with ice-cold 1 × PBS, harvested by centrifugation, and resuspended in 10 mL of ChIP lysis buffer I (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Igepal, 0.25% Triton X-100) in the presence of protease inhibitors cocktail (Sigma) for up to 10 minutes on ice. Next, the cells were suspended in ChIP lysis buffer II (10 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× protease inhibitor) for 10 minutes at room temperature. Fixed chromatin was sonicated into 200-500 bp fragments (Sonicator, Diagenode) in ChIP lysis buffer III (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1× protease inhibitor). Chromatin extracts were incubated with specific antibody (anti-Pol II, anti-Pol II-pSer2, anti-SPT5, anti-SPT5-CTR1/PRD, anti-NELFE, anti-AFF4) and protein A agarose beads at 4°C overnight. Immunoprecipitates were washed with RIPA buffer (50 mM HEPES-KOH [pH 7.5], 500 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate) for five times and TE twice. After the final wash, DNA was eluted with Elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1.0% SDS), and reverse-cross-linked at 65°C. Subsequently, the eluted DNA were treated with Protease K and RNase A, and were purified by FastPure Gel DNA Extraction Mini Kit (Vazymes).
ChIP-seq libraries were prepared using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazymes), and sequencing was performed using an Illumina NovaSeq 6000 platform

value: Human Colorectal Carcinoma Cells


title: 16S_G-RF1-T2

description: Library name: Sample 1

value: ruminal fluid

value: Grain-diet treatment


title: S.6704

value: (23-74970) Dual flanks


title: Patient sample 94

description:
Library name: P_94
Targeted RNA-Seq

value: FFPE


title: S.6701-L

value: Dual flanks


title: ChIP-seq SPT5_PSIP1ΔIBD


title: Patient sample 93

description:
Library name: P_93
Targeted RNA-Seq


title: Jsl1-150-2_1

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

institute: FU berlin

data_processing:
The raw sequenced reads were aligned to the human hg38 reference genome with STAR (v2.7.9a) default parameters in gene quantification mode. After this the software RSeQC v4.0.0 was used to check the stran used for sequencing. In this way only the 4th column of the star output was used to create the txt files.
Alternative splicing analysis was done with rMTAS turbo (v4.1.1), including variable-read-length criteria.
Assembly: hg38
Supplementary files format and content: contains STAR derived gene expression information in raw reads

growth_protocol: HEK293 and HeLa cells were maintained in DMEM High Glucose (Biowest), supplemented with 10% fetal bovine serum (FBS; Biochrom) and 1%  penicillin/streptomycin (BioWest). Jurkat JSL1 cells were maintained in RPMI 1640 (Biowest) supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Trizol (Bio&Sell) was used for RNA extraction as described in the user manual. Pure RNA was optained using DNAseI digestion and repurification. For the analysis of nascent transcripts, chromatin-associated RNA was isolated.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stimulated with 20ng/ml of phorbol myristate acetate (PMA, Sigma- Aldrich) or dimethyl sulfoxide (DMSO) as solvent control for different time points depending on the experiment setup. For morpholino experiments, heLa or HEK293 cells were seeded and transfected 1 day later using EndoPorter following the manufacturer’s manual.

value: PMA 150 minutes


title: Patient sample 92

description:
Library name: P_92
Targeted RNA-Seq

extract_protocol: Patient tissue samples were obtained during standard of care treatment from various clinical timepoints and were sent to HTG Molecular Diagnostics, Inc. for targeted sequencing using their HTG EdgeSeq Oncology Biomarker Panel (OBP) consisting of 2549 cancer-associated genes. Raw data was assembled from five batches of separate HTG runs


title: ChIP-seq SPT5-pCTR1_HCT116


title: S.6701


title: Jsl1-150-1_1


title: S.6742

value: JURV (1e7 x times) + anti-PD-1


title: Jsl1-30-2_1

value: PMA 30 minutes


title: ChIP-seq SPT5_HCT116


title: Patient sample 91

description:
Library name: P_91
Targeted RNA-Seq


title: Jsl1-30-1_1


title: ChIP-seq AFF4_PSIP1ΔIBD


title: Patient sample 90

description:
Library name: P_90
Targeted RNA-Seq


title: S.3899

value: liver cancer


title: 16S_G-RF1-T10

description: Library name: Sample 3


title: ChIP-seq AFF4_HCT116


title: Jsl1-NS-2_1

value: non-stimulated


title: S.3897


title: Patient sample 89

description:
Library name: P_89
Targeted RNA-Seq


title: ChIP-seq SPT5-pCTR1_HCT116_SPT5ΔPLD


title: S.6767

value: Anti-PD-1 (10mg/kg x 6 doses)


title: Jsl1-NS-1_1


title: Patient sample 88

description:
Library name: P_88
Targeted RNA-Seq


title: ChIP-seq SPT5-pCTR1_HCT116_WT


title: Patient sample 87

description:
Library name: P_87
Targeted RNA-Seq


title: S.6756


title: AdrenocorticalTumor_enzymatic_5

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1.  (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started)
Assembly: Genome assemblyGRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single cells were isolated from tissue samples using and enzymatic dissociation method. Approximately 5-250 mg of fresh tissue samples were washed in HBSS, thoroughly minced on ice, and placed in dissociating solution at 37°C with gentle pipetting every 5 minutes.  Tissue samples were dissociated with 25-30 ul enzyme D Multi Tissue Dissociation Kit (MTDK) (Miltenyi Biotec) or enzyme A Neural Tissue Dissociation Kit P (NTDK) (Miltenyi Biotec) or 2 mg/ml collagenase IV (Gibco, Thermo Fisher Scientific) or collagenase I (Gibco, Thermo Fisher Scientific) in 870 mM HBSS, 10% FBS, 20 mM HEPES for 20-30 minutes. Obtained homogenate was filtered in 3-5ml of Wash Buffer (1x DPBS, containing 10% FBS, 20mM HEPES, 6mM glucose) through a pre-wetted 70μm cell culture filter (Miltenyi Biotec) and centrifuged for 5 minutes at 300xg (4 °C).  After all, the pellet was resuspended in a Wash Buffer volume of 100-400 ul, depending on the pellet size.
Single cells were captured and barcoded, and cDNA libraries were generated using the Chromium Next GEM Single Cell 3ʹGEM, Library & Gel Bead Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. Final libraries were multiplexed and sequenced on an Illumina Novaseq 6000 / HiSeq2500 platform, using the S4 Reagent Kit v1.5.

value: adrenocortical tumor

value: enzymatic dissociation


title: ChIP-seq SPT5_HCT116_SPT5ΔPLD


title: Patient sample 86

description:
Library name: P_86
Targeted RNA-Seq


title: AdrenocorticalTumor_enzymatic_4

description: 10x Genomics


title: S.6723


title: ChIP-seq SPT5_HCT116_SPT5ΔPRD


title: Patient sample 85

description:
Library name: P_85
Targeted RNA-Seq


title: Brain, KO, 6

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

description:
Tet2KO_6
F

data_processing:
After demultiplexing, sequence data was checked for overall quality and yield. Then, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference genomes using the STAR aligner v.2.5.2b. The STAR aligner is a splice aware aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2 Only unique reads within exon regions were counted.
Assembly: mm10
Supplementary files format and content: raw counts

source_name: Brain

extract_protocol:
RNA was extracted from brains using the methods described above and total RNA was sent to Azenta Life Sciences (formally Genewiz) for library construction, sequencing and analysis. For this, RNA samples were firstly quantified using Qubit 2.0 Fluorometer (Life Technologies, CA, USA) and RNA integrity was measured using the RNA Screen Tape on Agilent 2200 TapeStation (Agilent Technologies, CA, USA). rRNA depletion was performed using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, MD, USA) according to the manufacturer’s protocol.
RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations. Briefly, enriched RNAs are fragmented for 15 min at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on 1 lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration.

value: Brain

value: Control HSC, Stroke


title: ChIP-seq SPT5_HCT116_WT


title: S.6722

value: JURV (1e7 x times)


title: Brain, KO, 5

description:
Tet2KO_5
E


title: S.6716


title: Brain, KO, 4

description:
Tet2KO_4
D


title: Patient sample 83

description:
Library name: P_83
Targeted RNA-Seq

data_processing:
Raw read counts received from HTG Molecular Diagnostics, Inc. are first bach effect corrected using combat R package and subsequntly normalized using edgeR Bioconductor package.
Supplementary files format and content: Data matrix with sample ID in rows and log2 normalized expression values in columns in a comma separated text file.


title: ChIP-seq Pol II_HCT116_SPT5ΔPRD

value: Human Colorectal Carcinoma Cells

value: Pol II


title: Brain, KO, 3

description:
Tet2KO_3
C


title: ChIP-seq Pol II_HCT116_SPT5ΔPLD


title: Patient sample 82

description:
Library name: P_82
Targeted RNA-Seq


title: S.6740

value: 50 ul PBS


title: Patient sample 81

description:
Library name: P_81
Targeted RNA-Seq


title: S.6753


title: Brain, KO, 1

description:
Tet2KO_1
A


title: ChIP-seq Pol II_HCT116


title: Patient sample 80

description:
Library name: P_80
Targeted RNA-Seq


title: Pig dorsal skin (unwounded, additional sequencing)

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

data_processing:
Base calls were converted to reads using the 10X Cell Ranger implementation of mkfastq and then aligned against the Sscrofa11.1 reference genome.
For quality control, scRNA-seq cell barcodes were restricted to those with 1000-5000 reads and less than 10% of their transcriptome from mitochondrial genes. Batch correction was performed to the 16 week data at the sample-level using anchor-based transfer in Seurat.
Assembly: Sus_scrofa.Sscrofa11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: dorsal skin wound

extract_protocol:
Skin wounds from porcine skin and xenografted human skin at POD 14 were harvested and mechanically digested with sharp dissecting scissors (n = 6 per condition). Tissue was then added to an enzymatic digestion solution consisting of Collagenase II (ThermoFisher, Cat:17101015) and IV (ThermoFisher, Cat:17104019) in DMEM-F12 (GIBCOTM, Fischer Scientific, Hampton, NH). Samples were digested on an orbital shaker at 150 rpm for 90 minutes at 37oC. FACS buffer was added to quench the digest and samples were filtered through 70 μm cell strainers. Samples were then centrifuged at 1500 for 5 minutes at 4°C and then filtered a second time using 40 μm cell strainers. scRNA-seq was then performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines. Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.
Transcriptomic samples were prepared from pooled single-cell suspensions using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, Chromium Single Cell B Chip Kit, and Chromium i7 Multiplex Kit (10X Genomics, cat# 1000075, 1000073, and 120262).

value: dorsal skin wound

value: all cells (unsorted)

value: Red duroc

value: Unwounded


title: ChIP-seq NELFE_HCT116_SPT5ΔPLD

value: NELFE


title: ChIP-seq NELFE_HCT116_SPT5ΔPRD


title: Patient sample 79

description:
Library name: P_79
Targeted RNA-Seq

value: FFPE


title: Patient sample 78

description:
Library name: P_78
Targeted RNA-Seq


title: Brain, WT, 5

description:
WT_5
5

value: Control


title: S.6732

value: liver cancer


title: ChIP-seq NELFE_HCT116


title: ChIP-seq AFF4_HCT116_SPT5ΔPLD


title: Patient sample 84

description:
Library name: P_84
Targeted RNA-Seq


title: Patient sample 77

description:
Library name: P_77
Targeted RNA-Seq


title: Brain, WT, 4

description:
WT_4
4


title: Pig dorsal skin, 4 weeks, wounded and treated with Verteporfin

value: Verteporfin, 4 weeks


title: ChIP-seq AFF4_HCT116_SPT5ΔPRD


title: Brain, WT, 3

description:
WT_3
3


title: Pig dorsal skin, 4 weeks, wounded and treated with PBS

value: PBS, 4 weeks


title: Patient sample 76

description:
Library name: P_76
Targeted RNA-Seq


title: Brain, KO, 2

description:
Tet2KO_2
B


title: ChIP-seq AFF4_HCT116_WT


title: Brain, WT, 2

description:
WT_2
2


title: Pig dorsal skin, 2 weeks, wounded and treated with Verteporfin

value: Verteporfin, 2 weeks


title: Brain, WT, 6

description:
WT_6
6

value: Brain


title: Patient sample 75

description:
Library name: P_75
Targeted RNA-Seq


title: Brain, WT, 1

description:
WT_1
1

value: Control HSC, Stroke


title: SHARP_KO_eV_for_36_2

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
The fastq files were quality and adapter trimmed using TrimGalore.
The fastq files were aligned using Hisat2.
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
Peak calling was done using Peakranger v.1.18 with a q-value cutoff < 0.0001. Peaks had be conserved in both replicates.
Assembly: hg19
Supplementary files format and content: Peaks as .bed files (generated from both replicates, and linked to the corresponding *_1 sample records)
Supplementary files format and content: Normalized coverage tracks as .bigwig files

source_name: HeLa

growth_protocol: Human HeLa cells were grown at 37°C with 5% CO2 in DMEM medium supplemented with 2% FCS and penicillin/streptomycin.

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907).
Lybrary-prep kit for ChIP-Seq: Diagenode MicropPlex Library Preparation kit v3.

value: HeLa

value: RBPSUH (D10A4) XP Rabbit mAb (Cell Signaling #5313)


title: Pig dorsal skin, 8 weeks, wounded and treated with Verteporfin

value: Verteporfin, 8 weeks