title: tissue, normal, patient 10

city: Xi’an, Shaanxi Province

first: SHEN

last: YAN

address: NO. 98 West Fifth Road

institute: Xi’an Jiaotong University

description: squamous cell

data_processing:
The original image data file obtained by Illumina high-throughput sequencing is transformed into the original sequencing sequence (SequencedReads) by CASAVA base recognition (BaseCalling) analysis, which are RawData or RawReads. The results are stored in FASTQ (fq) file format, which contains the sequence information of the sequencing sequence (reads) and the corresponding sequencing quality information.
The original data in fastq format is first processed by perl script to remove the connector sequence and filter out the reads with low quality (low quality, the number of bases with a base quality value less than or equal to 25 accounts for more than 5% of the total reads60%) and N (N means that the base information cannot be determined) to obtain clean reads that can be used for subsequent analysis.
HISAT 2.2.1 software was used to compare the clean reads with the reference genome to obtain the mapped reads for subsequent analysis.
FeatureCounts 2.0.2 software is used to calculate the number of read aligned to each gene, and the FPKM value of each gene is calculated according to the length of the gene.
The mapped reads were spliced with the Stringtie 2.2.0 software, and then compared with the reference genome GTF / GFF file using the Gffcompare-0.12.6 software to find the original unannotated transcribed region and to find new transcripts and new genes of the species.
Assembly: human NCBI genome build 36
Supplementary files format and content: geo_submission_gene.txt: Data in columns N1-N10 represent gene expression levels in normal tissues, and data in columns T1-T10 represent gene expression levels in tumor tissues.

source_name: adjacent normal tissue

extract_protocol:
The samples were taken out at -80 ℃ and immediately put into a liquid nitrogen precooled mortar. After adding liquid nitrogen to grind into powder, 50mg samples were weighed, 1ml TRizol was added, vortex mixing was carried out, 10min was placed at room temperature, 200ul chloroform was added, mixing was fully reversed for 15s, and 2-3min was placed at room temperature. 4 ℃, 12000rpm centrifuge 10min (pay attention to pre-cooling centrifuge), carefully absorb the supernatant of 400ul into a new EP tube, add isopropanol at 1:1 (V400ul V), vibrate and mix 15s 10min at 20 ℃, place 10min at 4 ℃, 12000rpm centrifuge 10min, discard the supernatant, wash the precipitation with 75% ethanol twice, centrifuge 1min at 4 ℃, thoroughly remove the supernatant, dry the centrifuge tube in a super clean table to transparent, add 40ul RNase-free water to dissolve. The concentration of the sample and the ratio of 260 to 280260 to 230 were measured and recorded by Nanodrop. The integrity of RNA was tested by Agilent 4150, and the sample was preserved at-80 ℃.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size -selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 ° C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Illumina Novaseq PE150.

value: adjacent normal tissue

tag: patient

tag: time

value: surgery


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D20, Tank P1, Salinity S20, replicate a

status: Public on Dec 01 2022

type: SRA

city: Fort Pierce

first: David

last: Bradshaw

state: FL

department: Aquaculture & Stock Enhancement

country: USA

institute: Florida Atlantic University at Harbor Branch Oceanographic Institute

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST20DP1a

library_source: transcriptomic

data_processing:
Sequenced reads from 57 RNA Seq libraries were imported into CLC Genomics Workbench (Qiagen, Hilden, Germany) where they were quality checked and trimmed to remove low quality and adapter sequences.
The resulting filtered, paired-end reads were then mapped to the S. dumerili reference genome (NCBI Genome: 12614) with > 74% mapping success. Gene expression values were calculated as transcripts per million (TPM).
Differentially expressed genes (DEGs) were calculated in the CLC Genomics Workbench and were defined as biologically significant with an absolute fold change ≥ 2 and statistically significant with an FDR p-value ≤ 0.05 when compared to expression under control conditions (30 ppt) within the same DPH.
Transcript-level counts, lengths, and TPM abundances were imported into R and converted to a gene-level set of tables using the library tximport/tximportData (1.18.0).
Genome_build: S. dumerili reference genome (NCBI Genome: 12614)
Supplementary_files_format_and_content: Raw transcript counts matrix from CLC Genomics
Supplementary_files_format_and_content: Raw gene counts matrix from CLC Genomics
Supplementary_files_format_and_content: DESeq2 variance stabilizing transformed transcript counts matrix
Supplementary_files_format_and_content: DESeq2 variance stabilizing transformed gene counts matrix
Supplementary_files_format_and_content: Transcript name to Entrez Gene ID matrix table

molecule: polyA RNA

organism: Trachinotus carolinus

source_name: whole body

growth_protocol: After hatching in a salinity of ~ 30 ppt, Florida pompano larvae were reared in 345 L tanks at one of three salinities (10, 20, 30 ppt) in triplicate. Larvae samples for RNA-seq and fatty acid analysis were collected every three days until weaning.

extract_protocol:
 Total RNA was extracted a set of homogenized larval samples using the Qiagen RNeasy Mini Kit and kept at -20°C. All extracts were checked for concentration (ng/µL) using a Qubit Fluorometer 3 (ThermoFisher Scientific, Waltham, MA, USA) and quality (A260/A280) using a ThermoFisher NanoDrop Spectrophotometer 2000.
Purified RNA samples were sent to GeneWiz (South Plainfield, NJ, USA) for high-throughput sequencing. Samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on one flowcell lane. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Whole fish (numbers varied with days post hatch) were placed into tubes containing RNAlater (Invitrogen, Waltham, MA, USA) stored at 4°C for 24 hours, and finally stored at -20°C until processed for nucleic acid extractions.

tag: days post hatch

tag: tank number

tag: salinity

tag: replicate

value: a

tag: feeding

value: Eart + MF


title: fDPC_P0_1

city: Guangzhou

first: Yuxin

last: Chen

address: Nanfang Dadao Street, Baiyun district

country: China

institute: Nanfang Hospital of Southern Medical University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq X Ten platform and single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 15 nt or longer than 35 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase. Randfold tools soft was used for novel miRNA secondary structure prediction.
Genome_build: hg18
Supplementary_files_format_and_content: tab-deimited text files include FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: hair follicles from human scalp

extract_protocol:
DPCs were isolated from human dermal papilla and cultured.Total RNAs of DPC-fresh, DPC-P0 and DPC-P3 were extracted and used for mRNA sequencing.
RNA quality was verified using an Agilent 2100 Bio-analyzer (Agilent Technologies, Santa Clara, CA). Libraries for mRNA sequencing were generated using the NEBNext Multiplex RNA Library Prep Kit for Illumina (NEB,USA) according to the manufacturer’s instructions.

tag: tissue

value: freshly isolated dermal papilla cells


title: S10-3-PEDV-IP-1

city: Hangzhou

first: Yaowei

last: Huang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.15)
The Fastq files were aligned to the reference genome (hg38,chlSab2 and PEDV) using TopHat (v2.1.1)
The m6A peak calling method was modified from published work.The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform.
For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
Sequence motifs on m6A peaks were identified by HOMER
Genome_build: hg38, chlSab2 and PEDV

source_name: human hepatoma cells

growth_protocol: S10-3 and MARC-145 cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics at 37 °C.

extract_protocol:
Total RNA was extracted form Mock or PEDV-infected samples using TRIzol reagent, and then mRNA was purified using the GenElute mRNA miniprep kit (Sigma) and fragmented by ZnCl2.Fragmented mRNA was incubated with anti-m6A antibody (Synaptic Systems).
Sample eluted RNA and input control libraries were constructed using a TruSeq stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s instructions.
MeRIP-seq

treatment_protocol: Cells were uninfected or infected with PEDV (MOI=0.1) for 24 hours

tag: cell type

value: human hepatoma cells

tag: antibody

value: Anti-m6A antibody

tag: treatment

value: PEDV infection for 24hpi


title: Prenatal, sample3, cortical plate

city: New York

first: Nadejda

last: Tsankova

state: New York

address: 1245 Madison Avenue

department: Pathology

institute: Icahn School of Medicine at Mount Sinai

description: nuclear RNA

library_source: transcriptomic single cell

data_processing:
Gene expression count matrices were generated with CellRnager(v3.1.5)
Seurat metadata was generated using Seurat(v4.0.4), Filtering step: i) Doublets were removed using DoubletFinder(v2.0.3) ii)Low quality nuclei removal (< 400 unique genes, < 1,000 UMI counts, or > 15% mitochondrial genes)
UMAP embeddings: "Dimensionality reduction was applied on the scaled expression of top 2,000 variable genes by Principal component analysis (PCA) (Seurat::RunPCA). To mitigate inter-sample technical variation when analyzing multiple samples, we normalized and integrated the data using the SCTransform workflow in Seurat, which finds mutual nearest neighbors (or anchors) to integrate different samples. PCA was re-computed using the top 3,000 variable features followed by nearest-neighbor graph construction (Seurat::FindNeighbors), unbiased Louvain clustering (Seurat::FindClusters), and Uniform Manifold Approximation and Projection (UMAP) (Seurat::RunUMAP) for visualization of the data in two dimensions."
Combined_log-normalized_AveExp_snRNAseq_Human.xlsx: Processed, log-normalized average gene expression data calculated for each of the following integrated objects: all prenatal germinal matrix samples, subclustered glia and progenitors from all prenatal germinal matrix samples, all prenatal cortical plate samples, subclustered glia and progenitors from 24-41gw samples, all adult SVZ+caudate samples, all adult neocortex samples. All clusters are also annotated by cell type / state. UMAPS of each object are included along with cell type abbreviations.
Assembly: GRCh38 human genome pre-mRNA transcriptome sequences
Supplementary files format and content: "barcodes.tsv.gz" contains barcodes sequences, "features.tsv.gz" contains feature ID and names, "matrix.mtx.gz" contains matrices with gene ID, cell ID and UMI information
Supplementary files format and content: "Seuratmetadata" files: comma separated file with Seurat metadata including barcode information, sample ID, nCounts_RNA, nFeatures_RNA, nCounts_SCT, nFeatures_SCT, percent.mt, and cell type annotations for each cluster of each sample
Supplementary files format and content: "UMAPembedding": comma separated file with UMAP cordinates
Supplementary files format and content: "Combined_log-normalized_AveExp_snRNAseq_Human.xlsx"; Excel sheet.

source_name: Brain, cortical plate

extract_protocol:
Tissues were dissociated by douncing 50-100 mg of prenatal tissue or 250 mg of adult tissue in 4 ml of lysis buffer (0.32 M sucrose, 5 mM calcium chloride, 0.1% Triton X-100, 0.1 mM ethylenediaminetetraacetic acid [EDTA], 3 mM magnesium acetate, and 1 mM dithiothreitol [DTT] in 1 mM Tris-HCl, pH 8.0) under RNase-free working conditions. Nuclei were isolated by sucrose gradient ultracentrifugation. RNA from single nuclei was prepared for sequencing using the 10X Genomics Chromium platform and the 3’ gene expression (3’ GEX) V3 kit, version 3.10. Each region and sample was barcoded and sequenced as separate libraries, without hashing. Nuclei were diluted and loaded with a target of 6,000 cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Primers containing Illumina read 1 (R1) sequencing primers, a 16-bp 10x Barcode, a 10-bp randomer and a poly-dT primer sequence were subsequently mixed with the nuclear suspension and master mix. After incubation of the GEMs, barcoded, full-length cDNA was generated from pre-mRNA. Then, the GEMs were broken and silane magnetic beads were used to remove leftover biochemical reagents and primers.
P5 and P7 primers, a sample index, and Illumina read 2 (R2) sequencing primers were added to each selected cDNA during end repair and adaptor ligation. P5 and P7 primers were used for Illumina bridge cDNA amplification (http://10xgenomics.com). Libraries were quantified using the Agilent Bioanalyzer and sequenced into 2x100 paired-end reads using the Illumina NovaSeq platform to target 50,000-100,000 reads per nucleus.

value: Brain, cortical plate

tag: developmental stage

value: 19 weeks gestation

tag: Sex

value: male

value: postmortem, non-pathological


title: HCT116, CTRL, UT, rep1

city: Singapore

first: Raghuvaran

last: Shanmugam

state: Singapore

address: 61 Biopolis Dr, Proteos,

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Base quality assessment of raw sequence was performed using FastQC v0.11.8 and Trimmomatic v0.32 was used to filter low quality bases and adapter sequences.
Spliced alignment was performed using HISAT2 with reference to Homo sapiens (GRCh38) genome index.
Gene-level expression counts were quantified (strand-specific read counting) using featureCounts (subread-v1.6.2 package).
Differential genes expression analysis was performed by using edgeR v3.26.4 package.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts of every gene for all samples.

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS (Gibco), penicillin and streptomycin (Gibco).

extract_protocol: NEBNext ultra II RNA directional library preparation

treatment_protocol: DMSO or SP2509 (3 uM) for 48 hours

tag: cell line

tag: disease state

value: colon cancer

value: untreated

tag: genotype

value: Wildtype


title: LAPA 3

city: Hang Zhou

first: Zhifei

last: Xu

address: 866 Yuhangtang Road

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited xls files include RPKM values for each sample.

source_name: HaCaT Cells

extract_protocol:
Cell culture supernatant was removed and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.

value: Lapatinib-treated

value: 24 h after treatment


title: tissue, normal, patient 9

description: squamous cell

value: adjacent normal tissue


title: tissue, normal, patient 8

description: squamous cell

value: surgery


title: HCT116, SP2509, rep1


title: LAPA 2


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D18, Tank P8, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST18DP8a

value: a


title: S10-3-PEDV-IP-2


title: LAPA 1


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D20, Tank P7, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST20DP7a

value: Eart + MF


title: tissue, normal, patient 7

description: squamous cell


title: S10-3-PEDV-Input-2


title: fDPC_P0_2

value: freshly isolated dermal papilla cells


title: tissue, normal, patient 6

description: squamous cell


title: Control 3

value: Control


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D18, Tank P7, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST18DP7a


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D18, Tank P6, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST18DP6a


title: Control 2


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D18, Tank P9, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST18DP9a


title: Control 1


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D18, Tank P4, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST18DP4a


title: S10-3-Ctrl-IP-2

value: human hepatoma cells

value: Anti-m6A antibody

value: No treatment


title: tissue, normal, patient 2

description: squamous cell


title: ST6KO-3

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Triple negative breast cancer

growth_protocol: DMEM complete +10% FBS, 1% Pen-strep; in an incubator at 37 C and 5% CO2

extract_protocol:
Total RNAs were isolated from cells using Trizol according to the manufacturer's protocol.
Illumina TruSeq Total RNA-Seq Library Prep

treatment_protocol: Lentivirus were infected into MDA-MB-231 cells with 3PFU/cell using Polybrene (Millipore) according to the manufacturer's protocol.

value: MDA-MB-231 cells

tag: grna carrier

value: Lenti virus


title: tissue, normal, patient 4

description: squamous cell

tag: patient


title: ST6KO-2


title: tissue, normal, patient 3

description: squamous cell

tag: time


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D18, Tank P1, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST18DP1a

tag: days post hatch


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D18, Tank P2, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST18DP2a

tag: tank number


title: tissue, normal, patient 5

description: squamous cell


title: S10-3-Ctrl-Input-1


title: tissue, normal, patient 1

description: squamous cell


title: ST6WT-2

value: wild type


title: S10-3-PEDV-Input-1

value: PEDV infection for 24hpi


title: RUES1-EPSC +Dox

city: Nankang

first: Jean

last: Lu

state: Taipei

address: 128 Academia Road, Section 2, IBMS, N401F

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: single-cell RNA

data_processing:
Cell Ranger count (10x Genomics)
All data was separately aligned to the custom human reference sequence and cells with > 0 tdTomato and BSD_WPRE counts were defined as human cells.
Genome_build: Ensembl Homo_sapiens.GRCh38.104 and Mus_musculus.GRCm39.104 reference genomes appended with exogenous tdTomato and BSD_WPRE sequences.
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every single cell

organism:
Homo sapiens
Mus musculus

source_name: Human-mouse chimera

growth_protocol: PODXL overexpression was induced by Dox treatment for 3 days in hEPSCs and then washed for 2 times with 1 xPBS. Single hPESCs were resuspended in N2B27-LCDM (5% KSR, 10 μM Y-27632) on ice for 30 minutes.To generate aggregated chimeras, 8-10 single hEPSCs and one 8C embryo  were brought together in a microwell within the drops of G-2TM PLUS (Vitrolife, 10132) media covered by paraffin oil (Merck Millipore, 1.07174.2500) for grwoth for additional ~37 hours.

extract_protocol:
Single cell was harvasted by enzymatic digest of whole chimera embryo, and suspended in 0.1% BSA/1 xPBS for subsequent library Construction.
Library preparation was performed according to workflow of 10x Genomics.
Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.12

treatment_protocol: About 120 embryos were pooled together for each condition (-Dox or +Dox)

value: Tet-on-PODXL hEPSC

value: with doxycycline (+Dox)

tag: mouse strain

value: ICR


title: tissue, tumor, patient 10

description: squamous cell

source_name: laryngeal tumor tissue

value: laryngeal tumor tissue


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D18, Tank P5, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST18DP5a

tag: salinity

tag: replicate


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P9, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP9a

tag: feeding

value: Art + EArt + MF


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P8, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP8a


title: S10-3-Ctrl-IP-1

tag: cell type


title: ST6WT-1


title: S10-3-Ctrl-Input-2


title: tissue, tumor, patient 9

description: squamous cell

tag: tissue

value: surgery


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P7, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP7a

value: a


title: tissue, tumor, patient 8

description: squamous cell


title: X35b

city: Utrecht

first: Emre

last: Kucukkose

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
UBEG pipeline (https://github.com/UMCUGenetics/IAP)
quality control on FastQ files (using FastQC)
align reads of each sample in a run against reference genome (using STAR) and add read groups (using Picard)
quality control on generated BAM files (using Picard)
count reads in features (using HTSeq-count
normalize read counts (using DESeq)
calculate RPKMs (using edgeR)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw, normalized and RPKM values for each Sample

growth_protocol: Colorectal cancer organoids were cultured and RNA was harvested as described previously (Küçükköse et al, JITC, 2022)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). A minimum of 50 μl at a minimal concentration of 4 ng/μl of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq RNA stranded polyA Library Prep Kit following manufacturer's protocols.

tag: origin

value: Organoid

tag: mmr

value: MSS

tag: braf status

value: Unknown


title: X34b

tag: cell line

tag: other names

value: Liver

value: MSI


title: RNApotII_TGF1

city: Shanghai

first: Haoyan

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

library_source: genomic

data_processing:
The FASTQ files were aligned to hg19 using Bowtie2. Enriched regions were determined by the MACS1.4 program
Genome_build: hg19
Supplementary_files_format_and_content: bed

molecule: genomic DNA

source_name: SW480 cells

growth_protocol: The human SW480 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
DNA were extracted by Phenol chloroform
chip-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CRC cells were cross-linked with 37% formaldehyde. Subsequently, the chromatin was sonicated and immunoprecipitated with various histone antibodies and IgG (CST, Massachusetts, U.S.).

value: human colorectal cancer cells

tag: passage


title: RNApotII_NC


title: H3K9ac_TGF


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P5, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP5a


title: tissue, tumor, patient 6

description: squamous cell


title: tissue, tumor, patient 7

description: squamous cell


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P4, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP4a


title: X33b


title: ST6KO-1

value: MDA-MB-231 cells

tag: genotype

tag: grna carrier


title: HCT116, siPIR, rep1

tag: disease state

value: colon cancer

tag: treatment

value: PIRIN Knockdown


title: H3K9ac_NC


title: X31b

value: Peritoneum


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P3, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP3a

tag: days post hatch

tag: tank number


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P2, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP2a

tag: salinity


title: H3K4m3_TGF


title: tissue, tumor, patient 4

description: squamous cell

tag: patient

tag: time


title: RUES1-EPSC -Dox

description: single-cell RNA

tag: cell type

value: Tet-on-PODXL hEPSC

value: without doxycycline (-Dox)

tag: mouse strain


title: H3K4m3_NC


title: tissue, tumor, patient 3

description: squamous cell

tag: tissue


title: H3K4m1_TGF


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P6, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP6a

tag: replicate

tag: feeding


title: X29b

tag: cell line

tag: origin

value: Caecum

tag: mmr

tag: braf status


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P9, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP9a

value: GW + Art + EArt


title: H3K4m1_NC

tag: passage


title: X27b

tag: other names

value: Tor1, MmC3

value: Lung

value: WT


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P8, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP8a

value: a


title: X32b


title: H3K36me3_TGF


title: X26b


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P7, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP7a


title: liver, patient11, week24

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

data_processing:
Unique molecular identifiers (UMIs) were generated using the CellRanger Pipeline version 3.1.0 (10x Genomics). Sequencing data were aligned to GRCh38-HBV reference genome.
CellRanger-processed filtered feature matrices were analyzed using Seurat version 3.2.3.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
After taking FNAs from the patients, samples were maintained on ice and immediately processed. After quality control steps, red blood cells were removed by 5 min incubation with Red Blood Cell Lysis Buffer (BioLegend) and subsequent 10x dilution with PBS. Cells were washed, counted, and subjected to scRNAseq.
Samples were prepared as outlined by the 10x Genomics Single Cell 5’ Reagent Kit user guide.
The molarity of each library was calculated based on library size as measured by the Bioanalyzer (Agilent Technologies) and qPCR amplification data. Samples were pooled and adjusted to 10 nM, then diluted to 2 nM. Each 2 nM pool was denatured. Library pools were further diluted to a final loading concentration of 14 pM. 150 μl were loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on the HiSeq 2500 (Illumina) system.

value: liver

tag: treatment

value: Tenofovir Alafenamide

tag: timepoint


title: tissue, tumor, patient 5

description: squamous cell

value: laryngeal tumor tissue

value: surgery


title: liver, patient11, week12


title: H3K36me3_NC

value: human colorectal cancer cells


title: X30b

value: MSI


title: liver, patient11, week0


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D15, Tank P1, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST15DP1a

tag: days post hatch

tag: tank number

value: Art + EArt + MF


title: X24b


title: liver, patient10, week24


title: H3K27m3_TGF


title: X28b


title: tissue, tumor, patient 1

description: squamous cell

tag: patient


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P6, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP6a

tag: salinity


title: tissue, tumor, patient 2

description: squamous cell

tag: time


title: H3K27m3_NC

tag: cell type


title: liver, patient10, week12

tag: tissue


title: X22b

value: Subcutaneous


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P5, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP5a

tag: replicate


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P3, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP3a

tag: feeding


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P4, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP4a


title: liver, patient10, week0

tag: cell line


title: H3K27ac_TGF


title: H3K27ac_NC


title: X23b

tag: origin


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P2, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP2a


title: liver, patient9, week24


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D12, Tank P1, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST12DP1a


title: X25b

value: Peritoneum

tag: mmr


title: X20b

value: Organoid

tag: braf status


title: H3K18ac_NC

tag: passage


title: X21b

tag: other names


title: X19b


title: liver, patient9, week0

tag: treatment


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D6, Tank P9, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST6DP9a

value: GW + Rot


title: H3K18ac_TGF


title: liver, patient9, week12

tag: timepoint


title: X18b


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D6, Tank P8, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST6DP8a

tag: days post hatch


title: pri-mir-124-plasmid_3

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description: expressed RNA after pri-mir-124 plasmid transfection

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, the reads were  mapped to the human genome (hg19) using tophat2 by requiring 3 edit distance (mismatch+indel) at maximum
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene ID and expression level in reads count for each sample

growth_protocol: HEK293 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq4000 by a 2X150 bp run.

treatment_protocol: Transfection experiments were conducted in HEK293 cells. Briefly, the transfection of pri-mir-124 plasmid and empty plasmid (negative control) were performed using lipfectamine 3000 (Invitrogen) according to the manufacturer’s protocol. HEK293 cells were plated in six-well plate to 50-60% confluence. For each well, pri-mir-124 plasmid (2μg) was added into 250 μL Opti-MEM medium (GIBCO BRL), 5μL lipofectamine 3000 into 250 μL Opti-MEM medium, and then mixed miRNA plasmid with lipofectamine 3000. The mixture was added to cells and incubated for 6 hours before replacing the medium. In parallel, negative control (2μg) transfection was conducted in the same way according to the manufacturer's instructions. Total RNA was prepared 48 hours after transfection. The RNA with polyA tails were isolated, ligated to the adapters, amplified, and sequenced following the standard RNAseq preparation protocol (Illumina, USA) with no modifications. The transfection experiments were conducted in triplicates.

value: highly transfectable derivative of human embryonic kidney 293 cells

tag: genotype/variation


title: pri-mir-124-plasmid_2


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D6, Tank P7, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST6DP7a

tag: tank number


title: liver, patient8, week24


title: liver, patient8, week12


title: X17b


title: pri-mir-124-plasmid_1


title: liver, patient8, week0


title: X16b

value: Caecum


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D6, Tank P6, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST6DP6a

tag: salinity


title: NC-plasmid_3

description: expressed RNA after empty plasmid transfection

value: empty plasmid


title: liver, patient4, week24


title: X15b


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D6, Tank P5, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST6DP5a


title: NC-plasmid_2


title: X14b


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D6, Tank P4, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST6DP4a


title: NC-plasmid_1


title: X13b


title: liver, patient4, week0


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D6, Tank P3, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST6DP3a


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D6, Tank P2, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST6DP2a


title: X12b


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P9, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP9a


title: 3-3 35mM glucose

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

data_processing:
adapter trimming with custom code using adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
reads aligned to human genome and transcript expression quantified using RUM
differentially expressed genes identified using EdgeR
Assembly: hg19
Supplementary files format and content: Results of differential expression analysis for two comparisons, raw read count, and quantile normalized log 2 read counts for visualization
Supplementary files format and content: 1 Gene: gene symbol,   2 Transcript: RefSeq transcript id,   3 Best: set to 1 for transcript with highest expression otherwise 0,   4 NonZero.Samples.N: number of samples with non-zero read counts for this transcript,   5 EDGE:A:log2:Proliferating_gluc-20mM_noPalm:Proliferating_gluc-05mM_noPalm: edgeR computed average log2 expression    6 EDGE:M:log2:Proliferating_gluc-20mM_noPalm:Proliferating_gluc-05mM_noPalm: edgeR computed log2 fold change    7 EDGE:pv:0-1:Proliferating_gluc-20mM_noPalm:Proliferating_gluc-05mM_noPalm: edgeR computed p-value   8 EDGE:FDR:0-1:Proliferating_gluc-20mM_noPalm:Proliferating_gluc-05mM_noPalm: edgeR+p.adjust computed false discovery rate   9 EDGE:A:log2:Proliferating_gluc-35mM_noPalm:Proliferating_gluc-05mM_noPalm: edgeR computed average log2 expression   10 EDGE:M:log2:Proliferating_gluc-35mM_noPalm:Proliferating_gluc-05mM_noPalm: edgeR computed log2 fold change  11 EDGE:pv:0-1:Proliferating_gluc-35mM_noPalm:Proliferating_gluc-05mM_noPalm: edgeR computed p-value  12 EDGE:FDR:0-1:Proliferating_gluc-35mM_noPalm:Proliferating_gluc-05mM_noPalm: edgeR+p.adjust computed false   13 QNLR-1-1 : quantile normalize log2 reads for sample 1-1  14 QNLR-1-2 : quantile normalize log2 reads for sample 1-2  15 QNLR-1-3 : quantile normalize log2 reads for sample 1-3  16 QNLR-2-1 : quantile normalize log2 reads for sample 2-1  17 QNLR-2-3 : quantile normalize log2 reads for sample 2-3  18 QNLR-3-1 : quantile normalize log2 reads for sample 3-1  19 QNLR-3-2 : quantile normalize log2 reads for sample 3-2  20 QNLR-3-3 : quantile normalize log2 reads for sample 3-3  21 Reads-1-1 : raw read count for sample 1-1  22 Reads-1-2 : raw read count for sample 1-2  23 Reads-1-3 : raw read count for sample 1-3  24 Reads-2-1 : raw read count for sample 2-1  25 Reads-2-3 : raw read count for sample 2-3  26 Reads-3-1 : raw read count for sample 3-1  27 Reads-3-2 : raw read count for sample 3-2  28 Reads-3-3 : raw read count for sample 3-3

growth_protocol: EndoC-βH2 cells were cultured as described (Albagli et al., 2019, PMID: 31208395)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.2 ug of total RNA was used for the construction of sequencing libraries.
Illumina sequencing libraries were constructed using the Illumina TruSeq stranded polyA kit according to manufactuer's protocol.

treatment_protocol: 3 days in 5.5mM (basal glucose level), 20mM (360mg/dl) or 35mM (630mg/dl) glucose (n=2-3 per condition)

value: human  embryonic beta cells

tag: growth status

value: proliferating

value: 35mM glucoase 3 days


title: X10b

value: Tor098, MmC1

value: Liver


title: X11b


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P7, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP7a

value: a


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P8, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP8a


title: 3-1 35mM glucose

tag: cell type


title: 2-3 20mM glucose

value: 20mM glucose 3 days


title: X9b


title: X8b


title: liver, patient4, week12

tag: tissue

value: liver

value: Tenofovir Alafenamide


title: 2-1 20mM glucose


title: 1-3 glucose 5.5mM control

value: control 3 days


title: X7b

value: MSI


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P5, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP5a

tag: replicate


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P4, Salinity S30, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP4a

tag: feeding


title: X6b

tag: cell line


title: 1-2 glucose 5.5mM control


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P3, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP3a


title: 3-2 35mM glucose


title: X5b

tag: origin


title: 1-1 glucose 5.5mM control


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P6, Salinity S10, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP6a


title: X4b

value: Subcutaneous

tag: mmr


title: (HK-2 cells, shPPM1K, Day10 3

city: Urumqi

first: Li

last: Zhang

address: the First Affiliated Hospital of Xinjiang Medical University, Urumqi,China

institute: Nephrology center of the First Affiliated Hospital of Xinjiang Medical University

data_processing:
FASTX-Toolkit (Version 0.0.13)
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13).
The short reads less than 16nt were also dropped.
After that, clean reads were aligned to the GRCh38 genome by HISAT2 (Kim, Langmead et al. 2015) allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)(Trapnell, Williams et al. 2010).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: human kidney-2 cells (HK-12)

growth_protocol: Human kidney-2 cells (HK-2) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNAs were extracted from HK2 cells using TRIzol Reagent following the methods by Chomczynski(Chomczynski and Sacchi, 1987). 2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina  following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: Hunan Youbao biological company was entrusted to construct PPM1K plasmid, the cells were cultured in serum-free medium, and 2.5 μG plasmid, add 100 μL incubate with opti MEM for 5min, and take 5 μL Lipofectamine ™  2000 join 100 μL opti MEM, incubate for 5min and mix the above reagents.

value: human kidney-2 cells (HK-12)

value: human kidney-2 cells (HK-2)

tag: genotype

value: PPM1K overexpress

value: Chronic kidney disease

tag: time

value: Day 10


title: BDC31_Healthy_HOAD173

type: RNA

city: Stanford

first: Stephen

last: Popper

state: CA

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

description: Note: the .gpr files do not contain probe or gene IDs. The rows in the gpr file correspond to the same order as in GPL20858. (ie, block 1 col 1 row 1 is ID 1, block 1 col 29 row 1 is ID29, block 1 col 1 row 2 is ID 30).

hyb_protocol: Samples were hybridized to Human Exonic Evidence Based Oligonucleotide (HEEBO) microarrays. at 65C for 14 hours.   Following hybridization arrays were washed in a series of four solutions containing 2XsSSC with 0.05% SDS, 2X SSC, 1X SSC, and 0.2 X sSSC.   Following the last wash, arrays were dried by centrifugation.

scan_protocol: Micorarrays were scanned using the AxonScanner4200AL (Molecular Devices).  Each element was located and the assocated data recorded using SpotReader (Niles Scientific).

data_processing: Data were filtered to exclude control and noncoding probes, background was calculated using the Edwards correction, data were normalized using a 2D spatial loess estimation, and replicate probes were averaged

source_name: Universal Reference RNA (Stratagene)

label_protocol: We amplified total RNA using the TargetAmmp Aminoallyl aRNA amplificaiton kit (Epicentre, Madison, WI). We labeled eight ug of amplified RNA and 5ug of amplified Universal Human Reference RNA (Agilent, Santa Clara, CA) using Cy5 and Cy3 dyes, respectively.

growth_protocol: Whole blood collected in PAXgene tubes

extract_protocol: Total RNA extracted using the PAXgene blood RNA kit (Qiagen)

tag: sample type

value: Universal Human Reference RNA (Stratagene)

source_name: whole blood RNA from Healthy individual, Cy5 labeled

value: whole blood

tag: disease state

value: Healthy

tag: age

tag: Sex

value: F

tag: days of fever


title: X3b

tag: other names

value: Tor098, MmC1

tag: braf status


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P2, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP2a

tag: days post hatch

tag: tank number

tag: salinity

value: a

value: GW + Rot


title: BDC38_Healthy_HOAD172

tag: tissue

value: M


title: 10371_DEN_HOAD167

source_name: whole blood RNA from patient with Dengue, Cy5 labeled

value: Dengue

value: Female


title: X2b

value: Organoid

value: MSI


title: N120_RT_HOAD171

source_name: whole blood RNA from patient with Rickettsia typhi, Cy5 labeled

value: Rickettsia typhi


title: N303_RT_HOAD166

value: Male


title: PM7, Conditioned, Rep3

city: Bangkok

first: Teerasak

last: E-kobon

address: 50 Ngam Wong Wan Rd, Lad Yao, Chatuchak

department: Department of Genetics

country: Thailand

institute: Kasetsart University

data_processing:
Reads were mapped to reference genome of P. multocida strain NCTC10322 using the bwa program version 0.7.17.4
Annotation process was done using the best-placed reference protein set and the GeneMarkS-2+ method in the NCBI prokaryotic Genome Annotation Pipeline (PGAP)
Mapped reads were counted using the samtools idxstats program version 1.10
Assembly: GCF_900187275.1

organism: Pasteurella multocida

growth_protocol: P. multocida were  growth in brain heart infusion broth at 37C 180 rpm for 10 hours

extract_protocol: Total RNA was harvested using TRIzol reagent (TRIGEN/MRC)

treatment_protocol: P. multocida were  growth in conditioned media from Aeromonas caviae at 37C 180 rpm for 10 hours

tag: strain

tag: treatment

value: Aeromonas conditioned media


title: BDC23_Healthy_HOAD169


title: PM7, Conditioned, Rep2


title: RNA sequencing of whole body Trachonitus carolinus larvae: Days Post Hatch D3, Tank P1, Salinity S20, replicate a

description:
clc_genomics_raw_transcript_counts.csv
clc_genomics_raw_gene_counts.csv
deseq2_vst_transcript_counts.csv
deseq2_vst_gene_counts.csv
transcript_to_gene_id.csv
LST3DP1a

tag: replicate

tag: feeding


title: BDC40_Healthy_HOAD168


title: 10437_EC_HOAD165

source_name: whole blood RNA from patient with E. coli, Cy5 labeled

value: E. coli


title: (HK-2 cells, shPPM1K, Day10 1

source_name: human kidney-2 cells (HK-8)

tag: cell line

value: human kidney-2 cells (HK-8)

tag: cell type

value: human kidney-2 cells (HK-2)

tag: genotype

value: PPM1K overexpress

value: Chronic kidney disease

value: Day 10


title: (HK-2 cells, shPPM1K, Day10 2

source_name: human kidney-2 cells (HK-10)

value: human kidney-2 cells (HK-10)

tag: time


title: (HK-2 cells, shControl, Day10 3

source_name: human kidney-2 cells (HK-6)

value: human kidney-2 cells (HK-6)

value: WT


title: PM7, Conditioned, Rep1


title: N367_ST_HOAD163

tag: sample type

value: Universal Human Reference RNA (Stratagene)

source_name: whole blood RNA from patient with S. typhi, Cy5 labeled

value: whole blood

tag: disease state

value: S. typhi

tag: age


title: (HK-2 cells, shControl, Day10 2

source_name: human kidney-2 cells (HK-4)

value: human kidney-2 cells (HK-4)


title: 11114_OT_HOAD164

source_name: whole blood RNA from patient with Orientia tsutsugamushi, Cy5 labeled

value: Orientia tsutsugamushi

tag: Sex

value: Female

tag: days of fever


title: X35a

tag: other names

tag: origin

value: Organoid

tag: mmr

value: MSS

tag: braf status

value: Unknown


title: X1b

value: Tor098, MmC1

value: MSI


title: PM2, Conditioned, Rep3

tag: strain

value: Aeromonas conditioned media


title: X34a

value: Liver


title: (HK-2 cells, shControl, Day10 1

source_name: human kidney-2 cells (HK-2)

value: human kidney-2 cells (HK-2)

tag: treatment

value: Chronic kidney disease

value: Day 10


title: PM2, Conditioned, Rep2


title: X33a


title: 10191_RT_HOAD161

tag: tissue

value: Rickettsia typhi


title: 10374_EC_HOAD160

value: Universal Human Reference RNA (Stratagene)

value: E. coli


title: Donor 6

city: Salt Lake City

first: Robert

last: Campbell

state: UT

institute: University of Utah

data_processing:
Optical duplicates were removed from Fastq files using clumpify (BBmap version 38.34) with an optical distance of 12000.
Sequencing adapters were trimmed from Fastq reads using cutadapt (version 1.16) with options -O 6 -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Trimmed reads were aligned to the human genome (version GRCh38, Ensembl release 98) using STAR (version 2.7.2c) with option --twopassMode Basic. The alignment index was built with STAR and option --sjdbOverhang 124.
Gene counts were collected using Subread featureCounts (version 1.6.3) using the Ensembl release 98 GTF annotation file and options -p -s 2  --largestOverlap.
Genes were filtered where the minimum count was <= 10 across all samples. DESeq2 (version 1.26.0) was run between treatment and control samples with independendentFiltering=FALSE and alpha=0.05. Log2 fold changes were generated with shrunken values.
Assembly: GRCh38
Supplementary files format and content: Filtered gene counts are provided in filtered_counts.txt for each sample. Genes are filtered for >= 10 counts in each sample. Gene differential results are in DESeq2_results.txt.

source_name: platelet

extract_protocol:
Trizol with RNA clean and concentrate
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Prep kit (20020595) and TruSeq RNA UD Indexes (20022371) .  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.

value: platelet

tag: subject status

value: healthy donor


title: Donor 5


title: X32a

tag: cell line

value: Peritoneum


title: PM7, Reference, Rep3

value: Control medium


title: PM2, Conditioned, Rep1


title: X31a


title: Donor 4


title: PM7, Reference, Rep2


title: 10307_DEN_HOAD159

value: whole blood

value: Dengue

value: Female


title: Donor 3


title: 10637_DEN_HOAD162


title: PM7, Reference, Rep1


title: X30a

value: Caecum


title: 10532_OT_HOAD158

value: Orientia tsutsugamushi

value: Male


title: BDC33_Healthy_HOAD147

value: Healthy

value: M


title: Donor 2


title: PM2, Reference, Rep3


title: N259_ST_HOAD146

value: S. typhi


title: X29a

value: MSI


title: 10584_OT_HOAD149


title: Donor 1


title: X27a

value: Tor1, MmC3

value: Lung

value: WT


title: Patient 6

value: platelet

value: non-viral sepsis patient

tag: infection

value: Escherichia coli


title: PM2, Reference, Rep1

value: Control medium


title: X26a

value: Peritoneum


title: Patient 4

value: Streptococcus viridans


title: X25a


title: X24a


title: Patient 5

value: Yeast


title: 78w TMJ disc, scRNAseq

city: Chengdu

first: Xianni

last: Yang

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: TMJ disc

extract_protocol:
To isolate TMJ disc cells, the discs were freed from the joint space and isolated precisely from the surrounding tissue using fine forceps and scissors under a stereomicroscope. Next, TMJ discs were digested in 4 mg/ml Pronase (10165921001, Roche, Switzerland) for one hour, followed by digesting in 2 mg/ml Collagenase P (11213857001, Roche, Switzerland) in fetal bovine serum (FBS)-free DMEM for 2 hours.
After filtering the cell suspension using 70 μm and 40 μm cell filters, the cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10x Chromium Controller. RNA from the barcoded cells was subsequently reverse-transcribed, and sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions. Sequencing was performed with an Illumina system.

treatment_protocol: Five-week-old  mice were anesthetized using an i.p. injection of tribromoethanol. The right cheek skin was prepared and sterilized with 70% ethanol and povidone-iodine solution. A vertical incision of less than 1 cm was made around the end of the zygomatic arch. Blunt tools were used to resect the muscles to expose the TMJ articular capsule. The TMJ disc was pinched at the anterior band with 31 Gauge needles. Muscle and skin were sutured with 6-0 Prolene sutures (DePuy Synthes, USA). Two weeks later, the animals were sacrificed for further analyses.

value: TMJ disc

value: 78 weeks old

tag: genotype

value: no


title: X28a


title: injury TMJ disc, scRNAseq

description: 10x Genomics

value: 7 weeks old

value: TMJ disc injury model


title: X23a

value: Caecum


title: 16w TMJ disc, scRNAseq

description: 10x Genomics

value: 16 weeks old


title: Patient 2

value: Staphylococcus aureus


title: Patient 1

value: Klebsiella pneumoniae


title: PM2, Reference, Rep2


title: 3w TMJ disc, scRNAseq

description: 10x Genomics

value: 3 weeks old

value: WT


title: X22a

value: Tor1, MmC3

value: Subcutaneous

value: MSI


title: BDC29_Healthy_HOAD144

value: Universal Human Reference RNA (Stratagene)

value: whole blood

value: Healthy

value: M


title: 3d TMJ disc, scRNAseq

description: 10x Genomics

value: TMJ disc

value: 3 days old


title: N102_ST_HOAD142

value: S. typhi

value: Male


title: X21a


title: N250_OT_HOAD145

value: Orientia tsutsugamushi

value: Female


title: TL28F

city: Besancon

first: Julien

last: Viot

address: 3 boulevard alexandre fleming

country: France

institute: CHU besancon

data_processing:
STAR v2.7.9a
FeatureCounts v2.0.1
Assembly: GENCODE Human Release 39 (GRCh38.p13)

source_name: Metastatic

extract_protocol:
Frozen samples from liver metastases of CRC retrieved surgically from 2009 to 2019 were used for mRNA extraction according to Qiagen Kit Qiagen AllPrep DNA/RNA Mini Kit (ref 80204manufacturer’s instructions.
The concentration of each library was measured by real-time PCR, samples with RIN score <7 according were discarded.
Constructed libraries were sequenced (200 cycles) in paired-end (2x100 bp) using a Novaseq 6000.

value: LIVER


title: X20a

value: Organoid


title: BDC22_Healthy_HOAD140


title: TL27C

source_name: Primary Tumor

value: COLON


title: N363_OT_HOAD139


title: X19a

value: WT


title: TJ9C


title: X18a

value: Peritoneum


title: TJ10F


title: 11452_RT_HOAD136

value: Rickettsia typhi


title: X17a

value: MSI


title: Striatum 175Q 26wk replicate 1

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

data_processing:
Illumina bcl2fastq2 v2.20.0 software used for basecalling.
FASTQ files were trimmed, aligned to the mouse reference genome (GRCm38), sorted, and counted using the Bulk RNAseq Analysis Pipeline from the Minnesota Supercomputing Institute’s Collection of Hierarchical UMII/RIS Pipelines (v0.2.0 was used for 26-week-old data. v0.2.2 was used for the 10-week-old data). Component steps for read trimming, aligning and counting are as follows:
Reads were trimmed with Trimmomatic v.0.33 using illumina adapters, seedMismatches=4,palindromeClipThreshold=15, simpleClipThreshold=7, minAdapterLength=2 and keepBothReads=true
Trimmed reas were aligned to GRCm38 using hisat v.2.1.0 using the parameters --rna-strandedness RF and --no-mixed (suppress unpaired alignments for paired reads).
Aligned reads were assinged to genes using the featureCounts function of Subread v.1.6.2 with the parameters -B -p -Q10 -s2 and the Ensembl GRCm38 v.97 annotation gtf.
Assembly: GRCm38
Supplementary files format and content: subread_counts_10wk.txt is a matrix of gene counts for each sample at 10 weeks of age
Supplementary files format and content: subread_counts_26wk.txt is a matrix of gene counts for each sample at 26 weeks of age

source_name: striatum

extract_protocol:
Collected tissue was stored in RNAlater solution (Thermo Fisher Scientific). Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific) following the manufacturer’s protocol. Quality control involved quantification using fluorimetry via RiboGreen assay kit (Thermo Fisher Scientific) and RNA integrity was assessed via capillary electrophoresis using an Agilent BioAnalyzer 2100 to generate an RNA integrity number (RIN).
Library creation was completed using oligo-dT purification of polyadenylated RNA, which was reverse transcribed to create cDNA. cDNA was fragmented, blunt ended, and ligated to barcode adaptors. Libraries were size selected to 320 bp ± 5% to produce average inserts of approximately 200 bp, and size distribution was validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen, Thermo Fisher Scientific) and qPCR. Libraries were then normalized, pooled, and sequenced on an S4 flow cell by an Illumina NovaSeq 6000 using a 150-nucleotide, paired-end read strategy. Libraries were prepared and sequenced in two batches based on mouse age; 10-week mice were sequenced to a minimum of 70 million reads/sample, while 26-week mice were sequenced to  a minimum pf 40 million reads/sample.

value: striatum

tag: gender

value: male

value: post natal week 26


title: Striatum 175Q 26wk replicate 3

value: female


title: Striatum 175Q 26wk replicate 2


title: N298_RT_HOAD143

source_name: Universal Reference RNA (Stratagene)

tag: sample type

value: Universal Human Reference RNA (Stratagene)

value: whole blood


title: Striatum 175QK772T 26wk replicate 4


title: SM78F


title: 10122_EC_HOAD135

tag: disease state

value: E. coli


title: N058_OT_HOAD138

tag: age


title: 11357_RT_HOAD132

tag: Sex


title: SM23C


title: Striatum 175Q 26wk replicate 4


title: Striatum 175QK772T 26wk replicate 3


title: N240_RT_HOAD137

tag: days of fever


title: X15a

tag: other names

value: Caecum


title: Striatum 175QK772T 26wk replicate 2


title: 9774_ST_HOAD129

value: S. typhi

value: Male


title: 10551_RT_HOAD130


title: X14a

tag: origin

value: Subcutaneous


title: SA49C


title: 10669_DEN_HOAD128

value: Dengue

value: Female


title: 10259_ST_HOAD131


title: X13a

tag: mmr


title: RN21C

value: COLON


title: 10672_DEN_HOAD127


title: X16a

tag: braf status


title: X12a

value: Organoid


title: RM62F

value: LIVER


title: RD84F


title: SA50F


title: RD83C


title: Striatum WT 26wk replicate 2

value: WT

tag: strain


title: X11a

value: MSI


title: X9a

value: Tor098, MmC1

value: Liver


title: Striatum WT 26wk replicate 4

value: striatum

value: male

value: post natal week 26


title: Striatum WT 26wk replicate 3

value: female


title: 11066_EC_HOAD122

value: Universal Human Reference RNA (Stratagene)

value: whole blood

value: E. coli


title: Striatum WT 26wk replicate 1


title: X10a


title: RC48F

tag: treatment


title: Striatum 175QK772T 26wk replicate 1

tag: tissue


title: 10639_DEN_HOAD117

value: Male


title: Hippocampus 175Q 26wk replicate 4

source_name: hippocampus

value: hippocampus


title: PJP64F


title: Hippocampus 175Q 26wk replicate 3


title: 10607_DEN_HOAD124

source_name: whole blood RNA from patient with Dengue, Cy5 labeled

value: Dengue

value: Female


title: 10262_DEN_HOAD119


title: X7a

value: Peritoneum


title: Hippocampus 175Q 26wk replicate 2


title: X6a

value: Caecum


title: PJ80F

value: LIVER


title: N372_ST_HOAD111

value: S. typhi


title: BDC26A_Healthy_HOAD110

source_name: whole blood RNA from Healthy individual, Cy5 labeled

value: Healthy

value: F


title: BDC27_Healthy_HOAD112

value: M


title: PG42F


title: Hippocampus 175Q 26wk replicate 1

value: male


title: PC36F


title: X5a

value: Tor098, MmC1

value: MSI


title: PC35C

value: COLON


title: X4a

value: Subcutaneous


title: X8a


title: BDC39A_Healthy_HOAD109

value: Universal Human Reference RNA (Stratagene)

value: whole blood


title: Hippocampus 175QK772T 26wk replicate 3

value: hippocampus

value: post natal week 26


title: N397_RT_HOAD108

source_name: whole blood RNA from patient with Rickettsia typhi, Cy5 labeled

value: Rickettsia typhi

value: Female


title: Hippocampus 175QK772T 26wk replicate 2

value: female


title: X2a

value: Organoid


title: Hippocampus 175QK772T 26wk replicate 1


title: X1a


title: OJ68F

value: LIVER


title: 11474_EC_HOAD106

source_name: whole blood RNA from patient with E. coli, Cy5 labeled

value: E. coli


title: OJ67C


title: Hippocampus WT 26wk replicate 4

value: WT


title: Hippocampus WT 26wk replicate 3


title: N248_OT_HOAD103

value: Orientia tsutsugamushi


title: N387_ST_HOAD104

value: S. typhi

value: Male


title: OA12F


title: Hippocampus 175QK772T 26wk replicate 4

value: male


title: fHCF, control, replicate 3

city: Oeiras

first: Daniel

last: Simão

address: Av. República, Qta. do Marquês, Estação Agronómica Nacional, Edificio IBET/ITQB

country: Portugal

institute: iBET, Instituto de Biologia Experimental e Biológica

data_processing:
Quality assessment of raw sequences and trimming were performed on the Lexogen’s QuantSeq data analysis pipeline – Bluebee. Sequences were mapped to the Ensembl Human Genome Assembly GRCh38 using the Bluebee platform (https://lexogen.bluebee.com/).
Transcriptome datasets were analyzed in Rstudio (version 4.0.4) using Bioconductor tools. Transcript counts were normalized using the DESeq2 package (Love, Huber and Anders, 2014) and annotated with AnnotationDbi package (Pagès H, Carlson M, Falcon S, 2021). Differential expression analyses were performed using DESeq2 by contrasting TGF-β-treated samples with control samples for each CF source individually.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files

source_name: fetal heart

growth_protocol: Human-induced pluripotent stem cells (hiPSCs) were differentiated into cardiac fibroblasts, based on previous reports (Bao et al., 2017; Zhang, Shen and Wu, 2020). Briefly, hiPSCs were propagated on surfaces coated with growth factor reduced phenol-red free Matrigel (BD Biosciences) in mTeSRTM1 medium (STEMCELL Technologies). At 80-90% of confluence, cells were passaged using Accutase (STEMCELL Technologies), seeded at 2-3×10^4cell/cm2, and cultured on mTeSRTM1 medium supplemented with 10 µM ROCK-specific inhibitor (Y-27632; TOCRIS). To start the differentiation hiPSCs were seeded at 2-3 × 10^5 cell/cm2 on 12-well plates. The first stage of differentiation, from hiPSCs into Cardiac Progenitor Cells (CPCs), was initiated three days after (day 0) by replacing the culture medium with RPMI 1640 basal medium (Thermo Fisher Scientific) supplemented with 6 µM CHIR99021 (TOCRIS). On day 1, the media was aspirated and replaced by RPMI 1640 basal medium. On day 3, the media was exchanged by a “combined medium” comprising of 1 mL of the spent media and 1 mL of freshly prepared RPMI 1640 basal medium supplemented with 2.5 µM IWP-2 (TOCRIS), per well. On day 5, the medium was replaced with RPMI 1640 medium. On day 6, the second stage of differentiation from CPCs to pro-epicardial cells started. hiPSC-CPCs were seeded at a density of 8×10^4 cell/cm2 on Synthemax II-SC (Corning®)-coated 12-well plates and cultured in LaSR medium (Advanced DMEM/F12 medium (Thermo Fisher Scientific), supplemented with GlutaMAX (Thermo Fisher Scientific), 100 mg/mL Ascorbic Acid (Sigma-Aldrich)), and 5 µM Y-27632 (TOCRIS)). From day 7 to day 8, medium was replaced by LaSR medium supplemented with 3 µM CHIR99021. From day 9 to day 11, medium was exchanged daily by LaSR medium. The last stage of differentiation, from pro-epicardial cells into cardiac fibroblasts (CF) started on day 12. Cells were seeded at a density of 3 × 10^4 cell/cm2 on 0.1% (w/v) Gelatin (Sigma-Aldrich)-coated 12-well plates and culture with FibroGROTM medium (Millipore Corporation), supplemented with 10 µg/mL RH-FGFb (R&D Systems) and 2 µM SB431542 (STEMCELL Technologies). From day 13 to day 18, medium was replaced daily by fresh FibroGRO medium supplemented with 10 µg/mL RH-FGFb and 2 µM SB431542. SB431542 was added daily. From day 18 onwards cells were passaged every 3 to 5 days using Accutase, for 5 to 7 min at 37°C, seeded at 5800 cell/cm2 on 0.1% (w/v) gelatin-coated 6-well plates, and cultures in FibroGROTM medium supplemented with 2 µM SB431542. SB431542 was added daily, and the medium was exchanged every two days. Human adult cardiac fibroblasts (aHCF) and human fetal cardiac fibroblasts (fHCF) were obtained from PromoCell (C-12375, Lot 436Z024.3) and Cell Applications (306K-05f), respectively. Cells were cultured in FibroGro LS complete media (Merk Millipore, SCMF002) supplemented daily with 2 µM SB431542 (Stem Cell Technologies, 72234), with media exchange every two days. Cells were passaged using accutase, seeded at 5800 cell/cm2 on 0.1% gelatin-coated surfaces. All cells were maintained at 37ºC under humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions, and quantified using a NanoDrop 2000c (Thermo Scientific). RNA quality was assessed using the Fragment Analyzer (Agilent). All samples passed quality control standards of minimum concentration and RNA Quality Indicator (RQN) > 9, with discrete 18S and 28S bands.
cDNA libraries were generated from 500ng of total RNA using the QuantSeq 3′ mRNA-Seq Library Prep FWD kit for Illumina (Lexogen) following the manufacturer’s instructions.

treatment_protocol: Cardiac fibroblasts were seeded at 5800 cell/cm2 on 0.1% gelatin-coated surfaces and cultured with FibroGro LS complete media supplemented daily with 2 µM SB431542, media was exchanged every two days. On day 4, media was replaced with FibroGro LS complete media supplemented with 10 ng/ml TGF-β1 (R&D systems) for activation or 2 µM SB431542 for control samples. Cells were further cultured for 48h.

value: fetal heart

tag: cell type

value: human fetal primary cardiac fibroblasts

value: Control (Non-activated)


title: fHCF, TGF-β1, replicate 3

value: TGF-Beta1 (Activated)


title: X3a

tag: cell line

value: Tor098, MmC1

value: Subcutaneous

value: MSI


title: OP82F


title: Patient 3

value: platelet

tag: subject status

value: non-viral sepsis patient

tag: infection

value: Enteric Gram Negative Rods isolated


title: Hippocampus WT 26wk replicate 2

value: hippocampus

tag: gender

value: post natal week 26

tag: genotype


title: Hippocampus WT 26wk replicate 1

value: female

value: WT


title: MJP56F

value: LIVER


title: OP81C

value: COLON


title: fHCF, TGF-β1, replicate 2


title: fHCF, control, replicate 2


title: Cortex 175Q 26wk replicate 4

source_name: cortex

value: cortex


title: 10039_OT_HOAD102

tag: sample type

value: Universal Human Reference RNA (Stratagene)

value: whole blood

tag: disease state

value: Orientia tsutsugamushi

value: Female


title: 10424_DEN_HOAD100

value: Dengue

tag: age

tag: Sex

value: Male


title: BDC35_Healthy_HOAD107

value: Healthy

value: F

tag: days of fever


title: BDC37_Healthy_HOAD101


title: MJ4F


title: 10653_OT_HOAD096


title: fHCF, TGF-β1, replicate 1

value: fetal heart

value: human fetal primary cardiac fibroblasts

value: TGF-Beta1 (Activated)


title: Cortex 175Q 26wk replicate 3

value: post natal week 26


title: MJ3C


title: fHCF, control, replicate 1

value: Control (Non-activated)


title: Cortex 175Q 26wk replicate 2

value: male


title: OA11C


title: MA60F

value: LIVER


title: MA44F


title: aHCF, control, replicate 3

source_name: adult heart ventricles

value: adult heart ventricles

value: human adult primary cardiac fibroblasts

value: WT


title: aHCF, TGF-β1, replicate 3


title: Cortex 175Q 26wk replicate 1

value: cortex


title: aHCF, TGF-β1, replicate 2


title: MA43C

value: COLON


title: Cortex 175QK772T 26wk replicate 3


title: Cortex 175QK772T 26wk replicate 4


title: 10375_OT_HOAD095

value: Universal Human Reference RNA (Stratagene)

value: whole blood

value: Orientia tsutsugamushi


title: aHCF, control, replicate 2


title: JPC20F


title: Cortex 175QK772T 26wk replicate 2

value: female


title: JPC19C


title: Cortex 175QK772T 26wk replicate 1


title: JMP74F


title: aHCF, control, replicate 1


title: 10654A_OT_HOAD091

value: Female


title: 10240_EC_HOAD090

value: E. coli


title: HP16F


title: hiPSC-CF, TGF-β1, replicate 3

source_name: hiPSC WTC

value: hiPSC WTC

value: hiPSC-derived cardiac fibroblasts


title: HP15C


title: hiPSC-CF, control, replicate 3


title: Mnase_spt6ldeltatSH2_rep3

city: Guangzhou

first: Chen

last: Chen

state: Guangdong

address: 723 Xinke Rd.

institute: South China Botanical Garden, Chinese Academy of Science

data_processing:
adapters were removed from raw sequencing reads with cutadapt (version 3.4, -m 10)
ChIP-seq reads were mapped to the Arabidopsis genome (TAIR10) by Bowtie2 with default settings
PCR duplicates were removed by using samtools (for pair-end reads) or running the MACS2-filterdup program (for single-end reads)
To identify read-enriched regions (peaks), the MACS2 program was employed to perform peak calling with the following settings (-g 135000000, -nomodel, and -p 0.01).
Highly confident peaks were generated by running idr (2.0.3) (--idr-threshold 0.01) with biological replicates
bigWig files were generated using bamCoverage with RPGC normalization
The nucleosome positions were determined by applying the improved nucleosome-positioning algorithm iNPS with default settings. The smoothed bigwig files across biological replicates were generated by using dpos function in DANPOS3. Finally, MNase-seq data among samples were normalized by applying quantile normalization methods to normalize occupancy with Wiq function in DANPOS3
Assembly: TAIR10
Supplementary files format and content: Bigwig files.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were stratified in the dark at 4°C for 3 days before being sown on agar plates containing 2.22 g/L Murashige and Skoog basal medium with vitamins mix (Cat. M519, PhytoTech LABS), 1.5% sucrose (pH 5.75), and 0.8% agar. Plant growth was in long-day photoperiod (16h light/8h dark cycles) at 22°C

extract_protocol:
plants were crosslinked with 1% formaldehyde for 20 min under vacuum at room temperature and quenched with 0.125 M glycine under vacuum for an additional 5 min. Approximately 500 milligrams of tissues were used for each ChIP assay. The chromatin was sonicated using a Covaris M220 sonicator (peak power: 75; duty factor: 20; cycles/burst: 200) for 210 s at 6°C. The lysates were centrifuged at 18,000 g for 10 min at 4°C to remove debris. 10 µL of supernatant was used as the input sample, whereas the remaining supernatant was kept for the downstream procedure. 10 µL of Dynabeads Protein A (Cat. 10002D, ThermoFisher SCIENTIFIC) were added to each sample to prewash for 1 h at 4°C with gentle rotating. ChIP was carried out using antibodies as follows: anti-GFP (Cat. ab290, Abcam) and anti-Pol II CTD repeat YSPTSPS (Cat. ab817, Abcam). 40 µL of Dynabeads Protein A were mixed with 4 µL of antibodies and incubated for approximately 6 h on a rotator at 4°C to form antibody-bead complexes. Finally, ChIP-DNA were recovered by Phenol/chloroform extraction. Approximately 400 milligrams of seedlings were used per sample. Additionally, equal amounts of spike-in nuclei extracted from Saccharomyces cerevisiae were added to each sample before MNase treatment, which worked as the internal control among samples. For MNase treatment, the prepared nuclei were resuspended in prewarmed MNase digestion buffer, followed by the addition of 8 units of MNase (Cat. 2910A, TaKaRa) and incubation (15 min at 37°C with periodic agitation). Finally, the mono-nucleosomal DNA was isolated from 2% agarose gels and quantified by the Qubit dsDNA HS assay kit (Cat. Q32851, ThermoFisher SCIENTIFIC).
ChIP libraries were prepared by using the NEBNext® Ultra™ DNA Library Prep Kit (E7370S) following the manufacturer’s instructions, and subsequently used for Illumina

treatment_protocol: 10-day old seedlings

value: seedlings

tag: chip antibody


title: 11379A_RT_HOAD088

value: Rickettsia typhi


title: Cortex WT 26wk replicate 3

value: post natal week 26


title: aHCF, TGF-β1, replicate 1

value: TGF-Beta1 (Activated)


title: 11106_OT_HOAD089

source_name: whole blood RNA from patient with Orientia tsutsugamushi, Cy5 labeled


title: 10608_DEN_HOAD084

value: Dengue

value: Male


title: Cortex WT 26wk replicate 1

value: WT


title: Cortex WT 26wk replicate 2

value: cortex

value: male


title: 10528_DEN_HOAD093

value: Universal Human Reference RNA (Stratagene)


title: 10205_DEN_HOAD086

value: whole blood


title: HB85F

value: LIVER


title: 10663_DEN_HOAD082


title: hiPSC-CF, TGF-β1, replicate 2


title: hiPSC-CF, control, replicate 2

value: Control (Non-activated)


title: Medulla 175Q 26wk replicate 4

source_name: medulla

value: medulla

value: female


title: Mnase_spt6l_rep3


title: MNase_WT_rep3


title: 11184_RT_HOAD081


title: GR70F


title: Cortex WT 26wk replicate 4


title: MNase_WT_rep2


title: hiPSC-CF, TGF-β1, replicate 1

value: hiPSC WTC


title: hiPSC-CF, control, replicate 1

value: hiPSC-derived cardiac fibroblasts


title: SYD-GFP spt6ldeltatSH2 rep3

value: seedlings

value: anti-GFP (Abcam, ab290)


title: GS54F


title: Medulla 175Q 26wk replicate 3

value: post natal week 26


title: Medulla 175Q 26wk replicate 2


title: GR18F


title: SYD-GFP rep3


title: GR69C

value: COLON


title: GD32F


title: Medulla 175QK772T 26wk replicate 4


title: spt6l SYD-GFP rep3


title: spt6l SYD-GFP rep2


title: Medulla 175QK772T 26wk replicate 3


title: CN39C


title: Medulla 175QK772T 26wk replicate 1


title: spt6l SYD-GFP rep1


title: spt6l SYD-GFP input


title: CN40F


title: CM38F


title: PDX3_MLL-AF10_MEN1-T349M_VTP50469_Menin-ChIP

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

description:
CBAM44728-iMENINres_ChIP_MEN1_VTP_0_1pct_chow_14d_REP1_211115_TGACCA_S19
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human(Gencode GRCh38/hg38) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM  atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and ngs.plot (pileup heatmaps). ChIPseq peaks were called using MACS2 with appropriate input samples used as controls.
TSS signals were assessed using the bedtools coverage function. Signal values were normalized based on the ratio of hg38-aligning reads in treated and control samples, after deduplication.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Sample signal files for visualization in IGV (.tdf), MACS peak calling output (.xls) and summary bedtools TSS signal intensities (xlsx)

source_name: MLL-AF10 rearranged human leukemia PDX (CBAM44728)

growth_protocol: MV4;11 cells were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). For the treatment the cells were plated at 2x10^5 cells/ml in T75 tissue culture treated flasks. Cryo-conserved PDX material was transplanted into non-conditioned NOG mice (250.000 cells per mouse) and harvested from bone marrow of tibias, femurs, iliac crests and lumbar spine after 14 days of drug- or vehicle-treatment.

extract_protocol:
PDX-derived human leukemia cells from the bone marrow were depleted for mouse cells using magnetic cell sorting (mouse cell depletion kit, Milteny). The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehide (methanol free) for 5 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was cheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquote of sherared chromatin to decrosslink in order to test completeness of shearing. Chromatin was considered passed QC if fragments 100-600bp were >90%. For immunoprecipitation we used aproximately chromatin from 1-10x10^6 cells, 5-10ug of specific antibody and 10-20ul of Protein-A/G magnetic beads (Dynal). In 16 hours the immune complexes were wased in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads.
1-10 ng of ChIP'ed DNA was used for Illumina compatibl library generation using ThruPlex DNA-seq kit with 12 to 14 cycles of amplification with single or paired end barcodes

treatment_protocol: ChIPseq for Menin and MLL1 was performed in MV4;11 cells harboring a MEN1-M327I mutation and in an MLL-AF10 rearranged PDX with MEN1-T349M as well as the respective isogenic WT controls. Drug treatments were performed for 4 days in vitro for with different doses of SNDX-5613 (0.1uM, 1uM, 5uM) or DMSO control. Treatment of the MLL-AF10 PDX CBAM44728 was performed by oral exposure in vivo using 0.1% VTP-50469 supplemented rodent diet for 14 days.

tag: chip-antibody

value: anti-Menin (Rb)

tag: antibody manufacturer

value: Bethyl laboratories

tag: antibody catalog number

tag: treatment molecule

tag: treatment timepoint

tag: treatment dose

value: 0.1% drug supplemented diet


title: PDX3_MLL-AF10_MEN1-WT_VTP50469_MLL1-ChIP

description:
CBAM44728_ChIP_MLL1_VTP_0_1pct_chow_14d_REP1_211115_GTTTCG_S13
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip

tag: cell line

value: anti-MLL1 (Rb)


title: PDX3_MLL-AF10_MEN1-T349M_vehicle_Menin-ChIP

description:
CBAM44728-iMENINres_ChIP_MEN1_vehicle_14d_REP1_211115_TTAGGC_S18
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip

value: vehicle

value: regular rodent diet


title: PDX3_MLL-AF10_MEN1-WT_vehicle_MLL1-ChIP

description:
CBAM44728_ChIP_MLL1_vehicle_14d_REP1_211115_GTGGCC_S12
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip


title: PDX3_MLL-AF10_MEN1-T349M_vehicle_MLL1-ChIP

description:
CBAM44728-iMENINres_ChIP_MLL1_vehicle_14d_REP1_211115_CGTACG_S14
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip


title: Medulla WT 26wk replicate 4

tag: tissue

value: male

value: WT

tag: strain


title: PDX3_MLL-AF10_MEN1-T349M_VTP50469_MLL1-ChIP

description:
CBAM44728-iMENINres_ChIP_MLL1_VTP_0_1pct_chow_14d_REP1_211115_GAGTGG_S15
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip


title: CM37C

tag: treatment


title: PDX3_MLL-AF10_MEN1-WT_VTP50469_Menin-ChIP

description:
CBAM44728_ChIP_MEN1_VTP_0_1pct_chow_14d_REP1_211115_CGATGT_S17
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip


title: Medulla WT 26wk replicate 3

tag: gender

tag: genotype


title: Medulla WT 26wk replicate 2


title: PDX3_MLL-AF10_MEN1-WT_vehicle_Menin-ChIP

description:
CBAM44728_ChIP_MEN1_vehicle_14d_REP1_211115_ATCACG_S16
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip


title: Medulla 175Q 26wk replicate 1


title: HTR5-GFP_MS_1_H2A.Z_IP

city: Beijing

first: Zhang

last: Huairen

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Reads were filtered for duplicated reads by using Picard version 2.24.0 MarkDuplicates
bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to input or sequencing depth using RPKM
Average ChIP-seq profiles were generated using deepTools utility plotProfile
Assembly: TAIR10
Supplementary files format and content: *.bw, normlized ChIP-seq coverage files

source_name: mature seeds

growth_protocol: Mature seeds, seeds imbibed for different time periods

extract_protocol:
Materials were ground with liquid nitrogen into fine powder and immediately fixed with 1% formaldehyde. Nuclei were extracted and mononucleosomes were generated with micrococcal nuclease (MNase) (Sigma, N5386) digestion as previously described. Immunoprecipitation was conducted with anti-GFP (Thermo Fisher Scientific, A-11122) or anti-H2A.Z. After antibody incubation, Protein A Dynabeads (Thermo Fisher Scientific, 10002D) were added to collect the immunocomplexes.
After washing, elution, reverse cross-linking and DNA purification, recovered DNA was subjected to library preparation with VAHTS universal DNA library prep kit for Illumina (Vazyme, ND607) according to the manufacture’s instruction

value: HTR5-GFP mature seeds

value: mature seeds


title: Medulla 175QK772T 26wk replicate 2

value: medulla

value: female


title: GD31C

source_name: Primary Tumor


title: CJ52F

source_name: Metastatic

value: LIVER


title: PDX3_MLL-AF10_ChIP-input

description:
CBAM44728_ChIP_input_steadystate_REP1_211115_GTGAAA_S11
PDX3_MLL-AF10__MEN1-WT-vs-T349M_TSS-signals.xlsx
PDX3_MLL-AF10__MEN1-WT-vs-T349M_Alignment-rmdup_STATs.zip


title: CF14F


title: HTR5-GFP_G24h_2_GFP_IP

source_name: imbibed seeds

value: HTR5-GFP seeds subject to germination for 24 hours

value: imbibed seeds

value: GFP


title: HTR5-GFP_G24h_1_GFP_IP


title: Medulla WT 26wk replicate 1

value: post natal week 26


title: HTR5-GFP_MS_2_H2A.Z_IP


title: CF13C

value: COLON


title: Cerebellum 175Q 26wk replicate 4

source_name: cerebellum

value: cerebellum


title: HTR5-GFP_S48h_2_GFP_IP

value: HTR5-GFP seeds stratified for 48 hours


title: CA26F


title: MV4;11_MEN1-M327_DMSO_MLL1-ChIP_SNDX5613_5uM

description:
MV411-MEN1-M327I_ChIP_MLL1_SNDX_5uM_4d_REP1_220115_GTCCGC_S16
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip

source_name: MLL-AF4 rearranged human leukemia cell line (MV4;11)

value: anti-MLL1 (Rb)

value: Bethyl laboratories


title: Cerebellum 175Q 26wk replicate 3


title: HTR5-GFP_S48h_1_GFP_IP


title: Cerebellum 175Q 26wk replicate 2


title: HTR5-GFP_MS_2_GFP_IP


title: MV4;11_MEN1-M327_DMSO_MLL1-ChIP_SNDX5613_1uM

description:
MV411-MEN1-M327I_ChIP_MLL1_SNDX_1uM_4d_REP1_220115_CCGTCC_S15
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: HTR5-GFP_MS_1_GFP_IP


title: BP66F


title: MV4;11_MEN1-M327_DMSO_MLL1-ChIP_DMSO

description:
MV411-MEN1-M327I_ChIP_MLL1_DMSO_4d_REP1_220115_AGTTCC_S13
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip

value: DMSO


title: Cerebellum 175Q 26wk replicate 1

value: male


title: BF8F


title: MV4;11_MEN1-M327_DMSO_Menin-ChIP_SNDX5613_0.1uM

description:
MV411-MEN1-M327I_ChIP_MEN1_SNDX_100nM_4d_REP1_220115_CAGATC_S6
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip

value: anti-Menin (Rb)


title: Cerebellum 175QK772T 26wk replicate 4


title: MV4;11_MEN1-M327_DMSO_Menin-ChIP_SNDX5613_5uM

description:
MV411-MEN1-M327I_ChIP_MEN1_SNDX_5uM_4d_REP1_220115_GATCAG_S8
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: BF7C


title: HTR5-GFP_G24h_1_input

value: input


title: Cerebellum 175QK772T 26wk replicate 3


title: MV4;11_MEN1-M327_DMSO_MLL1-ChIP_SNDX5613_0.1uM

description:
MV411-MEN1-M327I_ChIP_MLL1_SNDX_100nM_4d_REP1_220115_ATGTCA_S14
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: BC86F


title: HTR5-GFP_S48h_2_input


title: MV4;11_MEN1-M327_DMSO_Menin-ChIP_SNDX5613_1uM

description:
MV411-MEN1-M327I_ChIP_MEN1_SNDX_1uM_4d_REP1_220115_ACTTGA_S7
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: BC72F


title: HTR5-GFP_S48h_1_input


title: CA25C


title: Cerebellum 175QK772T 26wk replicate 1


title: Cerebellum 175QK772T 26wk replicate 2


title: BC71C


title: MV4;11_MEN1-M327I_DMSO_Menin-ChIP_DMSO

description:
MV411-MEN1-M327I_ChIP_MEN1_DMSO_4d_REP1_220115_GCCAAT_S5
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: MV4;11_MEN1-M327I_DMSO_ChIP-input

description:
MV411-MEN1-M327I_ChIP_input_DMSO_4d_REP1_220115_CGTACG_S20
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: Cerebellum WT 26wk replicate 3

value: WT


title: HTR5-GFP_G24h_2_input


title: AS76F


title: HTR5-GFP_MS_1_input

value: HTR5-GFP mature seeds

value: mature seeds


title: MV4;11_MEN1-M327I_DMSO_IgG-ChIP

description:
MV411-MEN1-M327I_ChIP_IgG_DMSO_4d_REP1_220115_GTGGCC_S18
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip

value: Rabbit polyclonal IgG

value: Abcam


title: AE2F

value: LIVER


title: MV4;11_MEN1-WT_DMSO_MLL1-ChIP_SNDX5613_5uM

description:
MV411_ChIP_MLL1_SNDX_5uM_4d_REP1_220115_AGTCAA_S12
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: h3.3ko_MS_1 Bisulfite-seq

data_processing:
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with BS-Seeker2 version 2.1.8 using default parameters
Duplicated reads were filtered with Picard version 2.24.0 MarkDuplicates.
CG, CHG, and CHH methylation levels were calculated with CGmaptools (version 0.1.2)
Methylation data were visualized with ggplot2 in R (version 1.1.1106).
Assembly: TAIR10
Supplementary files format and content: .gz, DNA methylation level

growth_protocol: Mature seeds

extract_protocol:
Genomic DNA was extracted with Quick-DNA Plant/Seed Miniprep Kit (ZYMO, D6020).
200ng fragmented genomic DNA (200bp-500bp) was used for library preparation with VAHTS universal Pro DNA library prep kit for Illumina (Vazyme, ND608). NEBNext Multiplex Oligos for Illumina (NEB, E7535) were used for adapter ligation. After purification with VAHTS DNA Clean Beads (Vazyme N411), bisulfite conversion was performed with EZ DNA Methylation-Gold Kit (ZYMO, D5005), followed by DNA purification and PCR amplification.


title: MV4;11_MEN1-WT_DMSO_MLL1-ChIP_SNDX5613_0.1uM

description:
MV411_ChIP_MLL1_SNDX_100nM_4d_REP1_220115_GGCTAC_S10
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: Cerebellum WT 26wk replicate 1

value: female


title: AS75C


title: MV4;11_MEN1-WT_DMSO_MLL1-ChIP_SNDX5613_1uM

description:
MV411_ChIP_MLL1_SNDX_1uM_4d_REP1_220115_CTTGTA_S11
MV4;11_MEN1-WT-vs-M327I_TSS-signals.xlsx
MV4;11_MEN1-WT-vs-M327I_Alignment-rmdup_STATs.zip


title: Col_MS_2 Bisulfite-seq

value: Col


title: h3.3ko_MS_2 Bisulfite-seq


title: Cerebellum WT 26wk replicate 2

value: post natal week 26


title: AE1C

value: COLON


title: Striatum 175Q 10wk replicate 4

source_name: striatum

value: striatum

value: post natal week 10


title: Striatum 175Q 10wk replicate 3


title: Striatum 175Q 10wk replicate 2


title: Col_MS_1 Bisulfite-seq